Effect of Different Treatment Technologies on the Fate of Antibiotic Resistance Genes and Class 1 Integrons when Residual Municipal Wastewater Solids are Applied to Soil

Exploring the historical roots, advantages and efficacy of phage therapy in plant diseases management

In the drug-resistance era, phage therapy has received considerable attention from worldwide researchers. Phage therapy has been given much attention in public health but is rarely applied to control plant diseases. Herein, we discuss phage therapy as a biocontrol approach against several plant diseases. The emergence of antibiotic resistance in agriculturally important pathogenic bacteria and the toxic nature of different synthetic compounds used to control microbes has driven researchers to rethink the century-old strategy of phage therapy''. Compared to other treatment strategies, phage therapy offers remarkable advantages such as high specificity, less chances of drug resistance, non-harmful nature, and benefit to soil microbial flora. The optimizations and protective formulations of phages are significant accomplishments; however, steps towards a better understanding of the physiologic characteristics of phages need to be preceded to commercialize their use. The future of phage therapy in the context of plant disease management is promising and could play a significant role in sustainable agriculture. Ongoing research will likely affirm the safety of phage therapy, ensuring that it does not harm non-target organisms, including beneficial soil microbes. Phage therapy could become vital in addressing global food security challenges, particularly in regions heavily impacted by plant bacterial diseases. Efforts to create formulations that enhance the stability and shelf-life of phages will be crucial, especially for their use in varied environmental conditions.

Stimulating the biofilm formation of Bacillus populations to mitigate soil antibiotic resistome during insect fertilizer application

Antibiotic resistance in soil introduced by organic fertilizer application pose a globally recognized threat to human health. Insect organic fertilizer may be a promising alternative due to its low antibiotic resistance. However, it is not yet clear how to regulate soil microbes to reduce antibiotic resistance in organic fertilizer agricultural application. In this study, we investigated soil microbes and antibiotic resistome under black soldier fly organic fertilizer (BOF) application in pot and field systems. Our study shows that BOF could stimulate ARB (antibiotic resistant - bacteria) - suppressive Bacillaceae in the soil microbiome and reduce antibiotic resistome. The carbohydrate transport and metabolism pathway of soil Bacillaceae was strengthened, which accelerated the synthesis and transport of polysaccharides to form biofilm to antagonistic soil ARB, and thus reduced the antibiotic resistance. We further tested the ARB - suppressive Bacillus spp. in a microcosm assay, which resulted in a significant decrease in the presence of ARGs and ARB together with higher abundance in key biofilm formation gene (epsA). This knowledge might help to the development of more efficient bio-fertilizers aimed at mitigating soil antibiotic resistance and enhancing soil health, in particular, under the requirements of global "One Health".

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.

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.

Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure

The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.

Coastal mudflats as reservoirs of extracellular antibiotic resistance genes: Studies in Eastern China

Despite coastal mudflats serving as essential ecological zones interconnecting terrestrial/freshwater and marine systems, little is known about the profiles of antibiotic resistance genes (ARGs) in this area. In this study, characteristics of typical ARGs, involving both intracellular (iARGs) and extracellular ARGs (eARGs) at different physical states, were explored in over 1000 km of coastal mudflats in Eastern China. Results indicated the presence of iARGs and eARGs at states of both freely present or attached by particles. The abundance of eARGs was significantly higher than that of iARGs (87.3% vs 12.7%), and their dominance was more significant than those in other habitats (52.7%-76.3%). ARG abundance, especially for eARGs, showed an increasing trend (p < 0.05) from southern (Nantong) to northern (Lianyungang) coastal mudflats. Higher salinity facilitated the transformation from iARGs to eARGs, and smaller soil particle size was conducive to the persistence of eARGs in northern coastal mudflats. This study addresses the neglected function of coastal mudflats as eARGs reservoirs.

Current trends in management of bacterial pathogens infecting plants

Plants are continuously challenged by different pathogenic microbes that reduce the quality and quantity of produce and therefore pose a serious threat to food security. Among them bacterial pathogens are known to cause disease outbreaks with devastating economic losses in temperate, tropical and subtropical regions throughout the world. Bacteria are structurally simple prokaryotic microorganisms and are diverse from a metabolic standpoint. Bacterial infection process mainly involves successful attachment or penetration by using extracellular enzymes, type secretion systems, toxins, growth regulators and by exploiting different molecules that modulate plant defence resulting in successful colonization. Theses bacterial pathogens are extremely difficult to control as they develop resistance to antibiotics. Therefore, attempts are made to search for innovative methods of disease management by the targeting bacterial virulence and manipulating the genes in host plants by exploiting genome editing methods. Here, we review the recent developments in bacterial disease management including the bioactive antimicrobial compounds, bacteriophage therapy, quorum-quenching mediated control, nanoparticles and CRISPR/Cas based genome editing techniques for bacterial disease management. Future research should focus on implementation of smart delivery systems and consumer acceptance of these innovative methods for sustainable disease management.

Ferric chloride further simplified the horizontal gene transfer network of antibiotic resistance genes in anaerobic digestion

The role of ferric chloride (FC) on the reduction of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) system was investigated from the perspective of vertical (VGT) and horizontal gene transfer (HGT) network through the high-throughput qPCR (HT-qPCR). Although FC showed limited impacts on methane production in AD of swine manure, the tetracycline and MLSB resistance genes were specifically reduced at the end, where tetQ of antibiotic target protection and ermF of antibiotic target alteration contributed the most to the reduction. Both VGT and HGT network were divided into three modules, and the complexity of HGT network was largely reduced along with AD, where the HGT connection was reduced from 683 (Module III) to 172 (Module I), and FC addition could further reduce the relative abundance of ARG hosts in Module I. The contribution of VGT and HGT to the changes of ARGs in AD was further deciphered, and although the VGT reflected by the changes of microbial community contributed the most to the dynamics of ARGs (68.0 %), the HGT contribution could further be reduced by the FC addition. This study provided a new perspective on the fate of ARGs response to the FC addition in the AD system.

Diverse antibiotic resistance genes and potential pathogens inhabit in the phyllosphere of fresh vegetables

Fresh vegetables are considered as a reservoir of pathogenic bacteria and antibiotic resistance genes (ARGs), which are the emerging environmental contaminants, posing increasing concerned risk to human health. However, the prevalence of pathogens in phyllosphere of fresh vegetables, as well as the association of ARGs with pathogenic bacteria, have not been well elaborated. In this study, we explored the structure of microbial communities and ARGs through high-throughput quantitative PCR and 16S rRNA gene Illumina sequencing, and characterized the microorganisms resisting to antibiotics by pure culture. From phyllosphere of six different kinds of vegetables, 205 ARGs were detected and genes for multidrug resistance was the most abundant. The predominant potential pathogens were classified to Pseudomonas, Klebsiella, and Acinetobacter genera, which carried various ARGs such as multidrug and beta-lactam resistance genes presumedly. Among six kinds of vegetables, Lactuca sativa var. asparagina carried the highest abundance of potential pathogens and ARGs, while Allium sativum L harbored the lowest abundance of pathogens and ARGs. In addition, various culturable bacteria resisting to colistin or meropenem could be isolated from all vegetables, remarkably, all the isolates resistant to both antibiotics are potential pathogens. Our study highlighted the risks of pathogens and ARGs from raw vegetables to consumers, characterized their structure patterns among different vegetables, and analyzed the potential mechanisms regulating phyllosphere pathogens and resistome of fresh vegetables, which would be helpful for reducing the microbial risk from vegetable ingestion.

Characteristics of antibiotic resistance genes in full-scale anaerobic digesters of food waste and the effects of application of biogas slurry on soil antibiotic resistance genes

The fate of antibiotic resistance genes (ARGs) in full-scale anaerobic digestion (AD) of food waste (FW) and in the soil applied with biogas slurry has not been fully understood. In this study, 12 targeted ARGs and intI1 in FW, intermediate product, and biogas slurry from three full-scale AD were analyzed. The results showed that subcritical water pretreatment was an effective method for ARG attenuation, by which the absolute abundance of total targeted ARGs was removed by 99.69%. The predominant ARGs (ermB, tetM, and tetW) in FW were removed more than 99% after subcritical water pretreatment. The result of field experiments with biogas slurry as fertilizer showed that the absolute abundance of several ARGs (sul2, tetM, blaOXA-1, blaTEM) and intI1 accumulated significantly compared to the control group (CK) during three consecutive growth stages of the rice. The detected abundance of ARGs in paddy field soil increased from 190.50 (CK) to 8.87 × 10⁴ copies/g (wet weight) (soil) during tillering stage, and increased from 4102.65 (CK) to 4.38 × 10⁴ copies/g (wet weight) (soil) during heading time. Biogas slurry improved the soil nutrients (TN, AN, TP, and AP); meanwhile, the concentrations of total salt and Cl^- increased. Network analysis indicated that 28 genera were the possible hosts of ARGs; variation partitioning analysis (VPA) indicated that microbial communities (contribution 59.30%) were the main factors that affected the fate of ARGs and intI1.

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.

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

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

Degradation of antibiotic resistance genes and mobile gene elements in dairy manure anerobic digestion

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins–Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.

Distance dilution of antibiotic resistance genes of sediments in an estuary system in relation to coastal cities

Coastal tourist and industrial cities are most likely to have differential effects on the distance dilution of antibiotic resistance genes (ARGs) in an estuary system. This study used high-throughput fluorescence quantitative polymerase chain reaction to identify sediment ARGs in two typical estuaries of coastal tourist and industrial cities (Xiamen and Taizhou) in China. The distance dilution of ARGs and its relationship with key environmental factors were analysed. The results indicated that along the river inlet towards the sea, the distance dilution effect on ARG abundance in estuary sediments of Taizhou was approximately double that in Xiamen, and the macrolide, lincosamide, and streptogramin B (MLSB) and vancomycin genes were replaced by the fluoroquinolone, quinolone, florfenicol, chloramphenicol, and amphenicol (FCA) and β-lactam genes in Taizhou, whereas β-lactam genes succeeded the MLSB and sul genes in Xiamen. The abundance and number of ARGs and mobile genetic elements (MGEs) were positively correlated with the particle size and total organic carbon (TOC) contents of sediments, whereas they were negatively associated with the oxidation and reduction potential (E_h) and pH of sediments, as well as the seawater salinity. The sediment particle size (SPZ) was the dominant physicochemical factor affecting the abundance of ARGs (r = 0.826, p < 0.05) and MGEs (r = 0.850, p < 0.01). These findings suggest that although the distance dilution effect on the ARG abundance of estuary sediments of the industrial city is greater than that of the tourist city, the larger SPZ, higher TOC content, and lower salinity, pH, and E_h in estuary regions adjacent to the industrial city can more significantly facilitate the proliferation and propagation of ARGs in the sediments.

Antibiotic resistance gene dissipation in soil microcosms amended with antibiotics and swine manure

The use of antibiotics in animal agriculture has exacerbated the presence of both antibiotic resistance genes (ARGs) and residual antibiotics excreted in animal manure. Field application of this manure is a common practice because its nutrient rich material can benefit crop growth. However, this practice can also introduce antibiotics and ARGs into nonagricultural settings. The integration of prairie buffer strips within and at the edge of crop fields is a potential management solution to reduce concentrations of ARGs commonly transported via water runoff and infiltration. An incubation experiment was conducted to investigate the fate of ARGs in directly manured crop field soils and the surrounding affected prairie strip soils. Row crop and prairie strip soils sampled from three sites received either an antibiotic spike and swine manure addition or a control water addition. The concentrations of select ARGs were then monitored over a 72-d period. Although soil vegetation and site location were not observed to influence ARG dissipation, the select genes did display different half-lives from one another. For example, tetM demonstrated the fastest dissipation of the genes quantified (average half-life, 5.18 d). Conversely, sul1 did not conform to the first-order linear regression kinetics used to describe the other investigated genes and was highly abundant in control prairie strip soils. The quantified half-lives of these select ARGs are comparable to previous studies and can inform monitoring and mitigative efforts aimed at reducing the spread of ARGs in the environment.

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

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

Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria

Antibiotic resistance (AR) is a threat to modern medicine, and plasmids are driving the global spread of AR by horizontal gene transfer across microbiomes and environments. Determining the mobile resistome responsible for this spread of AR among environments is essential in our efforts to attenuate the current crisis. Biosolids are a wastewater treatment plant (WWTP) byproduct used globally as fertilizer in agriculture. Here, we investigated the mobile resistome of biosolids that are used as fertilizer. This was done by capturing resistance plasmids that can transfer to human pathogens and commensal bacteria. We used a higher-throughput version of the exogenous plasmid isolation approach by mixing several ESKAPE pathogens and a commensal Escherichia coli with biosolids and screening for newly acquired resistance to about 10 antibiotics in these strains. Six unique resistance plasmids transferred to Salmonella typhimurium, Klebsiella aerogenes, and E. coli. All the plasmids were self-transferable and carried 3-6 antibiotic resistance genes (ARG) conferring resistance to 2-4 antibiotic classes. These plasmids-borne resistance genes were further embedded in genetic elements promoting intracellular recombination (i.e., transposons or class 1 integrons). The plasmids belonged to the broad-host-range plasmid (BHR) groups IncP-1 or PromA. Several of them were persistent in their new hosts when grown in the absence of antibiotics, suggesting that the newly acquired drug resistance traits would be sustained over time. This study highlights the role of BHRs in the spread of ARG between environmental bacteria and human pathogens and commensals, where they may persist. The work further emphasizes biosolids as potential vehicles of highly mobile plasmid-borne antibiotic resistance genes.

Simultaneously attenuating antibiotic resistance genes and improving the dewaterability of sewage sludge by conditioning with Fenton's reagent: the pivotal role of sludge pre-acidification

Fenton conditioning processes have been recently employed to improve the dewaterability of sewage sludge. However, it remains unclear whether the conditioning with Fenton's reagent would simultaneously attenuate antibiotic resistance genes (ARGs) in sludge and improve sludge dewaterability. It was found in the present study that sludge pre-acidification played a pivotal role in simultaneously removing ARGs and improving sludge dewaterability by conditioning with Fenton's reagent. When the sewage sludge was pre-acidified to pH = 3.0 and was then conditioned using Fenton's reagent, the absolute abundances of the total ARGs and the total mobile genic elements (MGEs) in conditioned sludge were reduced by 1.85-2.10 and 2.84-3.12 log units, respectively. Additionally, sludge capillary suction time (CST) and specific resistance to filtration (SRF) were drastically reduced, and the moisture content (MC) in dewatered sludge cake was reduced to only 60.61-69.95%. Such effective attenuation of ARGs and MGEs in conditioned sludge led to their removal in both the dewatered sludge cakes and dewatering filtrate. However, only the improvement of sludge dewaterability was attained by sludge conditioning with Fenton's reagent but without sludge pre-acidification. During the conditioning treatment, the removal of loosely bound extracellular polymeric substance (EPS) and tightly bound EPS in conditioned sludge contributed to the improvement of sludge dewaterability, and the damage of sludge microbial cells was highly correlated with the attenuation of antibiotic resistance. Thus, sludge pre-acidification combined with conditioning using Fenton's reagent can be employed to simultaneously attenuate the antibiotic resistance in sewage sludge and improve sludge dewaterability.

Alkaline-thermal pretreatment of spectinomycin mycelial residues: Insights on anaerobic biodegradability and the fate of antibiotic resistance genes

Alkaline-thermal (AT) pretreatment is an economical and efficient pretreatment method to improve anaerobic biodegradability of biowaste. This study investigated the effect of AT pretreatment of spectinomycin mycelial residues (SMRs) for promoting anaerobic biodegradability along with the reduction of antibiotic resistance genes (ARGs), and thus obtained the optimal conditions of AT pretreatment. Biomethane potential (BMP) test was conducted to evaluate the anaerobic biodegradability of untreated and pretreated SMRs, and the fate of ARGs was tracked by quantitative polymerase chain reaction. Results showed that the modified Gompertz model fitted the results of BMP tests satisfactorily. Furthermore, AT pretreatment promoted BMP (B₀) and reduced lag phase (λ) effectively. These were attributed to the solubilization of SMRs. The analyses of the changes in dissolved organic matter indicated that AT pretreatment could facilitate the solubilization of both biodegradable (e.g. protein) and recalcitrant matter (e.g. humic-like, analyzing by EEMs-PARAFAC), which had a significant corresponding positive (Person correlation, p < 0.01) and negative (Partial correlation, p < 0.01) influences on anaerobic biodegradability. However, the positive effects surpassed the negative effects, promoting the overall anaerobic biodegradability of SMRs. In addition, a considerable reduction of ARGs (by 0.62-1.36 log units) was observed at pH ≥ 12, attributed to the hydrolysis of phosphodiester bond of DNA in strong alkaline solution. Considering both anaerobic biodegradability and ARGs, the optimal AT condition was concluded as pH 12, temperature 90 °C and time 120 min.

Treatment Processes for Microbial Resistance Mitigation: The Technological Contribution to Tackle the Problem of Antibiotic Resistance

Advances generated in medicine, science, and technology have contributed to a better quality of life in recent years; however, antimicrobial resistance has also benefited from these advances, creating various environmental and health problems. Several determinants may explain the problem of antimicrobial resistance, such as wastewater treatment plants that represent a powerful agent for the promotion of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG), and are an important factor in mitigating the problem. This article focuses on reviewing current technologies for ARB and ARG removal treatments, which include disinfection, constructed wetlands, advanced oxidation processes (AOP), anaerobic, aerobic, or combined treatments, and nanomaterial-based treatments. Some of these technologies are highly intensive, such as AOP; however, other technologies require long treatment times or high doses of oxidizing agents. From this review, it can be concluded that treatment technologies must be significantly enhanced before the environmental and heath problems associated with antimicrobial resistance can be effectively solved. In either case, it is necessary to achieve total removal of bacteria and genes to avoid the possibility of regrowth given by the favorable environmental conditions at treatment plant facilities.

Screening of Bacterial Endophytes Able to Promote Plant Growth and Increase Salinity Tolerance

Bacterial endophytes can colonize plant tissues without harming the plant. Instead, they are often able to increase plant growth and tolerance to environmental stresses. In this work, new strains of bacterial endophytes were isolated from three economically important crop plants (sorghum, cucumber and tomato) grown in three different regions in soils with different management. All bacterial strains were identified by 16S rRNA sequencing and characterized for plant beneficial traits. Based on physiological activities, we selected eight strains that were further tested for their antibiotic resistance profile and for the ability to efficiently colonize the interior of sorghum plants. According to the results of the re-inoculation test, five strains were used to inoculate sorghum seeds. Then, plant growth promotion activity was assessed on sorghum plants exposed to salinity stress. Only two bacterial endophytes increased plant biomass, but three of them delayed or reduced plant salinity stress symptoms. These five strains were then characterized for the ability to produce the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which is involved in the increase of stress tolerance. Pseudomonas brassicacearum SVB6R1 was the only strain that was able to produce this enzyme, suggesting that ACC deaminase is not the only physiological trait involved in conferring plant tolerance to salt stress in these bacterial strains.

Fate of antibiotic resistance genes during high-solid anaerobic co-digestion of pig manure with lignite

Lignite could be used to promote methane production during high-solid anaerobic co-digestion (HS-AcoD) of pig manure, however, the effects of lignite amendment on the fate of ARGs during HS-AcoD are unknown. Here, we explored the influence of lignite (0%, 8%, 16%, 32%, and 64%) on the fate of ARGs during HS-AcoD of pig manure. The results showed that 16% lignite reduced the absolute abundance of ARGs by 28.71% compared with the 0% lignite treatment. Variation partitioning analysis suggested the combined effect of microbial community, mobile genetic elements (MGEs) and environmental factors was the major driver shaping the pattern of ARGs. The potential hosts of ARGs were Bifidobacterium, Lactobacillus, Tissierella and Streptococcus. Structural equation models analysis suggested lignite indirectly impacted the pattern of ARGs by significantly reducing the abundance of microbial community and MGEs. These findings give an insight into the mechanistic understanding of the lignite influence on the reduction of ARGs during HS-AcoD.

Prevalence of Antibiotic Resistome in Ready-to-Eat Salad

Ready-to-eat salad harbors microorganisms that may carry various antibiotic resistance genes (ARGs). However, few studies have focused on the prevalence of ARGs on salad, thus underestimating the risk of ARGs transferring from salad to consumers. In this small-scale study, high-throughput quantitative PCR was used to explore the presence, prevalence and abundance of ARGs associated with serving salad sourced from two restaurant types, fast-food chain and independent casual dining. A total of 156 unique ARGs and nine mobile genetic elements (MGEs) were detected on the salad items assessed. The abundance of ARGs and MGEs were significantly higher in independent casual dining than fast-food chain restaurants. Absolute copies of ARGs in salad were 1.34 × 10⁷ to 2.71 × 10⁸ and 1.90 × 10⁸ to 4.87 × 10⁸ copies per g salad in fast-food and casual dining restaurants, respectively. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were the dominant bacterial phyla detected from salad samples. Pseudomonas, Acinetobacter, Exiguobacterium, Weissella, Enterobacter, Leuconostoc, Pantoea, Serratia, Erwinia, and Ewingella were the 10 most dominant bacterial genera found in salad samples. A significant positive correlation between ARGs and MGEs was detected. These results integrate knowledge about the ARGs in ready-to-eat salad and highlight the potential impact of ARGs transfer to consumers.

Conditioning with zero-valent iron or Fe2+ activated peroxydisulfate at an acidic initial sludge pH removed intracellular antibiotic resistance genes but increased extracellular antibiotic resistance genes in sewage sludge

Sulfate radical (SO₄^-)-based conditioning methods, such as zero-valent iron (ZVI, i.e., Fe⁰) or ferrous iron (Fe²⁺) activated peroxydisulfate (S₂O₈^2-), have recently developed to improve sludge dewaterability, but it remains unclear how they impact the intracellular and extracellular antibiotic resistance genes (ARGs) in sewage sludge. In this study, it was found that conditioning treatments that used ZVI/S₂O₈^2- or Fe²⁺/S₂O₈^2- system, at an acidic initial sludge pH, removed the intracellular ARGs and intI1 and the extracellular intI1 from sewage sludge, but led to the accumulation of extracellular ARGs of aadA-01, aadA-02, aadA1, aadA2-03, and strB in conditioned sludge. During sludge conditioning with ZVI/S₂O₈^2- or Fe²⁺/S₂O₈^2-, bacterial hosts of ARGs and intI1 were seriously lysed to release the intracellular ARGs and intI1 to the extracellular environment, thus removing intracellular ARGs and intI1 in sludge, while the released ARGs and intI1 were primarily degraded by the produced SO₄^- to attenuate most extracellular ARGs and intI1. However, the relatively lower degradation ability of SO₄^- for extracellular ARGs of aadA-01, aadA-02, aadA1, aadA2-03, and strB led to their accumulation in conditioned sludge. Therefore, SO₄^--based conditioning methods can be employed to reduce ARGs in sludge, but the subsequent treatment of sludge dewatering filtrate requires more attention.

Host identity determines plant associated resistomes

Plant microbiome, as the second genome of plant, and the interface between human and environmental microbiome, represents a potential pathway of human exposure to environmental pathogens and resistomes. However, the impact of host identity on the profile of resistomes in plant phyllosphere is unclear and this knowledge is vital for establishing a framework to evaluate the dissemination of antibiotic resistance via the plant microbiome. Here, we explored the phyllosphere microbiome and resistomes in 12 selected plant species. By using High-throughput quantitative PCR, we identified a total of 172 unique resistance genes in plant phyllosphere microbiome, which was significantly divergent from the profile of resistomes in associated soils (Adonis, P < 0.01). Host identity had a significant effect on the plant resistome, which was mainly attributed to the dissimilarity of phyllosphere bacterial phylogeny across different plants. We identified a core set of plant resistomes shared in more than 80% of samples, which accounted for more than 64% of total resistance genes. These plant core resistomes conferred resistance to antibiotics that are commonly administered to humans and animals. Our findings extend our knowledge regarding the resistomes in plant phyllosphere microbiome and highlight the role of host identity in shaping the plant associated antibiotic resistance genes.

Engineering a CRISPR Interference System To Repress a Class 1 Integron in Escherichia coli

Microbial multidrug resistance (MDR) poses a huge threat to human health. Bacterial acquisition of MDR relies primarily on class 1 integron-involved horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). To date, no strategies other than the use of antibiotics can efficiently cope with MDR. Here, we report that an engineered CRISPR interference (CRISPRi) system can markedly reduce MDR by blocking a class 1 integron in Escherichia coli Using CRISPRi to block plasmid R388 class 1 integron, E. coli recombinants showed halted growth upon exposure to relevant antibiotics. A microplate alamarBlue assay showed that both subgenomic RNAs (sgRNAs) R3 and R6 led to 8- and 32-fold decreases in half-maximal inhibitory concentrations (IC50) for trimethoprim and sulfamethoxazole, respectively. Reverse transcription and quantitative PCR (RT-qPCR) revealed that the strain employing sgRNA R6 exhibited 97% and 84% decreases in the transcriptional levels of the dfrB2 cassette and sul1, two typical ARGs, respectively. RT-qPCR analysis also demonstrated that the strain recruiting sgRNA R3 showed a 96% decrease in the transcriptional level of intI1, and a conjugation assay revealed a 1,000-fold decrease in HGT rates of ARGs. Overall, the sgRNA R3 targeting the 31 bp downstream of the Pc promoter on the intI1 nontemplate strand outperformed other sgRNAs in reducing integron activity. Furthermore, this CRISPRi system is reversible, genetically stable, and titratable by varying the concentration of the inducer. To our knowledge, this is the first report on exploiting a CRISPRi system to reduce the class 1 integron in E. coli This study provides valuable insights for future development of CRISPRi-based antimicrobial agents and cellular therapy to suppress MDR.

Seasonal variations in antibiotic resistance genes in estuarine sediments and the driving mechanisms

Estuary sediments are chemically contaminated by adjacent coastal industrial cities, but the impact of organic pollutants on antibiotic resistance genes (ARGs) in estuarine sediments is unknown. We comprehensively analyzed the complex interactions between chemical pollutants (heavy metals and organic pollutants), mobile genetic elements (MGEs), and ARGs in estuarine sediments during various seasons. The results indicate that under the effects of the chemically polluted river water, the number of different estuarine sediment ARGs increased by 76.9%-92.3% in summer and 5.9%-35.3% in winter, and the abundance of these ARGs increased by 29-5195 times in summer and 48-239 times in winter. The abundance of sediment ARGs in distinct estuaries showed different seasonal trends. Seasonal changes had a greater impact on the abundance of estuarine sediment ARGs than on their diversity. The diversity of estuarine sediment ARGs was positively correlated with the chemical pollution levels. Furthermore, chemical pollution was positively correlated with MGEs, and MGEs were correlated with ARG abundance. These results indicate that ARGs are enriched in bacteria via horizontal gene transfer triggered by chemical pollution, promoting multi-antibiotic resistance in estuarine sediment bacteria. These findings have implications for our understanding of the distribution and propagation of ARGs in chemically polluted estuarine sediments.

Effects of nanoscale zero-valent iron on the performance and the fate of antibiotic resistance genes during thermophilic and mesophilic anaerobic digestion of food waste

The effects of nanoscale zero-valent iron (nZVI) on the performance of food waste anaerobic digestion and the fate of antibiotic resistance genes (ARGs) were investigated in thermophilic (TR) and mesophilic (MR) reactors. Results showed that nZVI enhanced biogas production and facilitated ARGs reduction. The maximum CH₄ production was 212.00 ± 4.77 ml/gVS with 5 g/L of nZVI in MR. The highest ARGs removal ratio was 86.64 ± 0.72% obtained in TR at nZVI of 2 g/L. nZVI corrosion products and their contribution on AD performance were analyzed. The abundance of tetracycline genes reduced significantly in nZVI amended digesters. Firmicutes, Chloroflexi, Proteobacteria and Spirochaetes showed significant positive correlations with various ARGs (p < 0.05) in MR and TR. Redundancy analysis indicated that microbial community was the main factor that influenced the fate of ARGs. nZVI changed microbial communities, with decreasing the abundance bacteria belonging to Firmicutes and resulting in the reduction of ARGs.

Antibiotic resistance and class 1 integron gene dynamics along effluent, reclaimed wastewater irrigated soil, crop continua: elucidating potential risks and ecological constraints

Reuse of municipal wastewater is a growing global trend, but currently there is lack of consensus regarding the potential dissemination of antibiotic resistance elements by treated wastewater irrigation. We tracked intI1, a proxy for anthropogenic pollution, and an assemblage of antibiotic resistance genes associated with mobile elements and/or wastewater (bla_GES, bla_OXA2, bla_OXA10, bla_TEM, bla_CTX-M-32 and qnrS) in treated wastewater effluents, effluent stabilization reservoirs, and along irrigation water-soil-crop continua in experimental lysimeters and large-scale commercial fields. While several of the targeted antibiotic resistance genes were profuse in effluents, there was almost no correlation between gene abundance in irrigation water and those detected in soil, and no evidence of systematic gene transfer to irrigated soil or crops. In contrast, soil intI1 abundance correlated strongly to irrigation water levels in lysimeters and sandy field soils, but this was not the case for clay-rich soils or for most of the analyzed crops, suggesting that intI1 may not always be a reliable marker for tracking the impact of treated wastewater irrigation. We hypothesize that "ecological boundaries" expedited by biotic and abiotic factors constrain dissemination of antibiotic resistance elements, and assert that a more holistic perception of these factors is crucial for understanding and managing antibiotic resistance dissemination.

The correlation between antibiotic resistance gene abundance and microbial community resistance in pig farm wastewater and surrounding rivers

Antimicrobial resistance gene (ARG) abundance and microbial resistance (MR) are often used as important indicators of pollution risk; however, the relationship between ARGs abundance and MR in pig farm wastewater remains unknown. In this study, the raw pig farm wastewater, effluent water, upstream river water, domestic wastewater and downstream river water samples were collected. The concentration of 20 subtypes of ARGs and 2 integrons, minimal inhibit concentration (MIC), and bacterial communities were investigated. In this study, 20 subtypes of ARGs and integrons were detected in all sampling sites. The highest abundance of 17 of the 20 subtypes of ARGs was detected in raw pig farm wastewater, and ermA had the maximum average abundance of 10⁸ copies/mL, with up to 2.41 ± 0.12 × 10⁸ copies/mL. There was no significant correlation between MR to three antibiotics (ciprofloxacin, streptomycin and tetracycline hydrochloride) and the abundance of their corresponding ARGs (P > 0.05), and a large difference was detected between the types of ARGs co-occur bacteria and resistance co-occur bacteria in the 5 sampling sites. And the pig farm wastewater treatment (WWT) could effectively reduce the ARGs and MR to the 3 antibiotics. The results presented here show that there may be no obvious correlation between ARGs and MCR in pig farm wastewater and surrounding rivers, which may be due to various environmental factors, highlighting the urgent need for a comprehensive evaluation of relationship between ARGs abundance and MR.

Phyllosphere of staple crops under pig manure fertilization, a reservoir of antibiotic resistance genes

In China, the common use of antibiotics in agriculture is recognized as a potential public health risk through the increasing use of livestock derived manure as a means of fertilization. By doing so this may increase the transfer of antibiotic resistance genes (ARGs) from animals, to soils and plants. In this study two staple crops (rice and wheat) were investigated for ARG enrichment under differing fertilization regimes. Here, we applied 4 treatments, no fertilizer, mineral fertilizer, clean (reduced antibiotic practice) and dirty (current antibiotic practice) pig manure, to soil microcosms planted with either rice or wheat, to investigate fertilization effects on the abundance of ARGs in the respective phyllospheres. For both rice and wheat, samples were collected after two separate fertilization periods. In total, 162 unique ARGs and 5 mobile genetic elements (MGEs) were detected from all rice and wheat samples. The addition of both clean and dirty manure, enhanced ARG abundance significantly when compared to no fertilizer treatments (P < 0.001), though clean manure enriched ARGs to a lesser extent than dirty manure, in all rice and wheat samples (P < 0.001). The classes of ARGs recorded were different between crops, with wheat samples having a higher ARG diversity than rice. These results revealed that staple crops in China such as rice and wheat may be a reservoir for ARGs when clean and dirty pig manure is used for fertilization.

Synergistic effects of key parameters on the fate of antibiotic resistance genes during swine manure composting

Livestock manure is a reservoir of antibiotic resistance genes (ARGs), posing a potential risk to environment and human health. However, there has been no optimization study about the comprehensive composting treatment for livestock manure ARGs based on multiple operation factors. In this study, anaerobic composting of swine manure in light was conducted under different combined conditions of composting time, temperature, water content, pH, heavy metal passivators and wheat straw. The diversity and relative abundance of ARGs in the compost were detected using high throughput quantitative real-time PCR, and the concentrations of antibiotics and heavy metals were determined. The results showed that under the optimized conditions (composting time, 30 d; temperature, 50 °C; water content, 50%; pH 9.0; heavy metal passivators and wheat straw), compared with the control, the detected number of ARGs and mobile genetic elements in the compost was reduced by 45% and 27.3%, and their relative abundance decreased by 33.9% and 36.9%, respectively. Moreover, the exchangeable heavy metal content of the compost declined by 34.7-57.1%, and the antibiotic level decreased by 28.8-77.8%. This study proposes that synergistic effects of key parameters can effectively mitigate the combined contamination of ARGs, antibiotics, and heavy metals in swine manure. MAIN FINDING: Optimized parameters (anaerobic composting time 30 d, temperature 50 °C, water content 50%, pH 9.0) effectively mitigated the combined pollution of ARGs, antibiotics, and heavy metals in swine manure.

Sludge bio-drying followed by land application could control the spread of antibiotic resistance genes

The process of sludge bio-drying has been adopted in response to the increasing amount of residual sewage sludge. It has been demonstrated that sludge bio-drying effectively reduces both antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), whereas ermF, tetX, and sulII become enriched in response to the dynamic development of the microbial community. The present study further demonstrated that the land application of sludge bio-drying products under current application rate did not cause an increase in the abundance of quantified ARGs in the soil but the persistence of ARB should be paid attention. Although land application introduced ermF, tetX, and tetG into the soil, these soon decreased to control levels. Furthermore, the decay rate varied between soil types, with red soil being the most persistent based on kinetics modeling. The fate of ARGs could also be attributed to the dynamics of the microbial community during land application, and the genus Parasegetibacter, which can degrade extracellular DNA, might play a key role in the control of ARGs. In summary, sludge bio-drying following land application could constitute an effective means of controlling the spread of ARGs, and microbial community changes contributed the most to the fate of the ARGs during the entire treatment chain (residual sewage sludge → bio-drying process → land application).

A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment

The emerging contamination of pathogenic bacteria in the soil has caused a serious threat to public health and environmental security. Therefore, effective methods to inactivate pathogenic bacteria and decrease the environmental risks are urgently required. As a century-old technique, bacteriophage (phage) therapy has a high efficiency in targeting and inactivating pathogenic bacteria in different environmental systems. This review provides an update on the status of bacteriophage therapy for the inactivation of pathogenic bacteria in the soil environment. Specifically, the applications of phage therapy in soil-plant and soil-groundwater systems are summarized. In addition, the impact of phage therapy on soil functioning is described, including soil function gene transmission, soil microbial community stability, and soil nutrient cycling. Soil factors, such as soil temperature, pH, clay mineral, water content, and nutrient components, influence the survival and activity of phages in the soil. Finally, the future research prospects of phage therapy in soil environments are described.

The role of substrate types and substrate microbial community on the fate of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion (AD) is regarded as a promising technology in energy recovery and the spread mitigation of antibiotic resistance. However, the performance of AD is dependent on various factors, and substrate type is one of the most important. In this study, the fate of antibiotic resistance genes (ARGs) response to the substrate types was investigated, and three typical environmental reservoirs of ARGs (pig manure, chicken manure and sewage sludge) were selected. The role of substrate microbial community on the fate of ARGs was clarified through the comparison between the AD of the substrates with and without a prior autoclave-disinfected step. Results showed that substrate types significantly influenced the fate of ARGs, while the influence from the substrate microbial community was limited. The concentration of antibiotics, the horizontal gene transfer reflected by intI1 and co-selection from heavy metals reflected by metal resistance genes (MRGs) were all reduced effectively. Microbial community varied from substrate types and dominated the ARGs fate concerning the standardized total effects through the mantel test and SEM analysis. The fate of tetX, ermF, tetM and ermB was mainly determined by the physicochemical parameters and the phyla of Firmicutes and Bacteroides. The phyla of Actinobacteria, pcoA and czcA contributed most to the reduction of bla_TEM and mcr-1, and the phyla of Proteobacteria, Chloroflexi, Synergistetes, Euryarchaeote, intI1 and merA correlated significantly with the fate of bla_CTX-M, ereA, tetG and sulI. This study highlighted the importance of substrate types when considering the fate of ARGs during AD.

Metallic nanoparticles induced antibiotic resistance genes attenuation of leachate culturable microbiota: The combined roles of growth inhibition, ion dissolution and oxidative stress

The dissemination and propagation of antibiotic resistance genes (ARGs) is an emerging global health concern, and the potential effects of nanomaterials on ARGs fates have drawn much attention recently. In the current study, the effects of metallic nanoparticles on ARGs occurrence of leachate culturable microbiota were investigated by four typical metal and metal oxide nanoparticles (Cu, Zn, CuO, and ZnO). The ARGs diversity was remarkably decreased during the cultivation and enrichment of leachate microbiota, and their abundances decreased for 1.4-3.2 orders of magnitude. The presence of nanoparticles facilitated the ARGs attenuation, and the magnitude of effects depended on types of nanoparticles and ARGs. Metal oxide nanoparticles caused more remarkable effects than metal nanoparticles. Mechanism analysis indicated that bacterial growth was inhibited, and the dissolved metal ions from nanoparticles partially contributed to nanoparticles decreasing ARGs. Flow cytometry experiments further confirmed that nanoparticles could enter bacterial cells, and then induce excessive reactive oxygen species (ROS) generation and increase membrane permeability. Finally, the possible mechanisms were put forward, and the structural equation models (SEM) differentiated the contribution of different factors shaping ARGs. The dissolved metal ions and growth inhibition caused by nanoparticles decreased ARGs transfer frequencies via exerting excessive metal stress and lowering population density. On the other hand, nanoparticles were incorporated into the cells, and then induced the generation of ROS, which might facilitate ARGs horizontal transfer via increasing membrane permeability, or decrease ARGs via the damage of genomic and plasmid DNA. Therefore, nanoparticles could affect ARGs fates via several ways, and combined effects finally determined the ARGs variations.

Antibiotic Resistomes in Plant Microbiomes

Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.

Occurrence and contamination profiles of antibiotic resistance genes from swine manure to receiving environments in Guangdong Province southern China

Livestock farms are commonly regarded as the main sources of antibiotic resistance genes (ARGs), emerging pollutants with potential implications for human health, in the environment. This study investigated the occurrence and contamination profiles of nine ARGs of three types from swine manure to receiving environments (soil and water) in Guangdong Province, southern China. All ARGs occurred in 100% of swine manure samples. Moreover, the absolute concentration of total ARGs varied from 3.01 × 10⁸ to 7.18 × 10¹⁴ copies/g, which was significantly higher than that in wastewater and manured soil (p < 0.05). Regarding the distribution characteristics of ARGs in swine manure, wastewater and manured soil, the tetracycline resistance gene tetO was predominant. ARGs in swine manure were relatively stable among swine growth periods after the nursery period. The ARG concentration did not differ significantly between manured and unmanured soil (p > 0.05). However, the number of ARGs (ermB, qnrS, acc(6')-Ib, tetM, tetO and tetQ) decreased but were not eliminated by wastewater treatment components (p < 0.05). Based on correlation analysis, the tetracycline resistance genes tetQ and tetW in swine manure and the macrolide resistance genes ermB and ermF in wastewater were more easily spread than were other ARGs onto soil when the substances were applied as fertilizers. Therefore, effective removal and a standard permissible environmental level of ARGs should be established to control the risk of spreading ARGs in the environment.

Anaerobic/aerobic conditions determine antibiotic resistance genes removal patterns from leachate by affecting bacteria taxa-genes co-occurrence modules

Landfill treatment of municipal solid waste treatment produces a large amount of leachate, which has been an important hotspot of ARGs. This study aimed to investigate the ARGs removal potential, kinetics and mechanism from leachate in aerobic and anaerobic conditions. Simulated landfill reactors showed the efficacy in reducing ARGs, and the removal efficiencies depended on ARGs types and aerobic/anaerobic conditions. The ARGs tetQ and bla_CTX-M were more likely to attenuate with the log-removal efficiencies of 1.50-3 order of magnitude. The ARGs removal kinetic was well fitted by modified Collins-Selleck model, and aerobic condition showed better removal capacities and kinetics than anaerobic condition. Among the ARGs with great removal performance, sul2, aadA1and bla_CTX-M were eliminated from leachate and refuse simultaneously, but tetM, ermB, and mefA were removed from leachate but enriched in refuse. Aerobic/anaerobic states might drive the bacterial community shift of leachate and refuse, and topology property comparison of co-occurrence networks suggested that refuse had a closer non-random host relationship between ARGs and microbial taxa than leachate. Further module analyses revealed that ARGs removal efficiencies depended on the taxonomy of host bacteria in leachate, while the refuse taxa-ARGs correlation determined ARGs removal patterns. By selecting distinct bacteria cluster in different conditions, aerobic treatment benefited ARGs reduction in leachate and refuse, while anaerobic treatment enhanced the enrichment of ARGs in refuse. These findings can potentially foster the understanding of ARGs removal mechanism in biological treatment processes.

Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting

About 1.3 billion tons of food waste (FW) is annually produced at a global scale. A major fraction of FW is deposited into landfills thereby contributing to environmental pollution and emission of greenhouse gasses. While increasing amounts of FW are recycled more sustainably into fertilizers in industrial-scale composting, very little is known about the antibiotic resistance genes (ARGs) present in FW and how their abundance is affected by composting. To study this, we quantified the diversity and abundance of ARGs, mobile genetic elements (MGEs) and bacterial communities in the beginning, during and at the end of the FW composting. All targeted 27 ARGs and 5 MGEs were detected in every sample suggesting that composted FW remains a reservoir of ARGs and MGEs. While the composting drastically changed the abundance, composition and diversity of bacterial communities, an increase in total ARG and MGE abundances was observed. Changes in ARGs were linked with shifts in the composition of bacterial communities as revealed by a Procrustes analysis (P < 0.01). Crucially, even though the high composting temperatures reduced the abundance and diversity of initially ARG-associated bacterial taxa, ARG abundances were maintained in other associated bacterial taxa. This was likely driven by horizontal gene transfer and physicochemical composting properties as revealed by a clear positive correlation between ARGs, MGEs, pH, NO₃^- and moisture. Together our findings suggest that traditional composting is not efficient at removing ARGs and MGEs from FW. More effective composting strategies are thus needed to minimize ARG release from composted FW into agricultural environments.

Comparing polyvalent bacteriophage and bacteriophage cocktails for controlling antibiotic-resistant bacteria in soil-plant system

Antibiotic resistant pathogenic bacteria (ARPB) residual in soil-plant system has caused serious threat against public health and environmental safety. Being capable of targeted lysing host bacteria, phage therapy has been proposed as promising method to control the ARPB contamination in environments. In this study, microcosm trials were performed to investigate the impact of various phage treatments on the dissipation of tetracycline resistant Escherichia coli K-12 and chloramphenicol resistant Pseudomonas aeruginosa PAO1 in soil-carrot system. After 70 days of incubation, all the four phage treatments significantly decreased the abundance of the pathogenic bacteria and the corresponding antibiotic resistance genes (tetW and cmlA) in the soil-carrot system (p < 0.05), following the order of the cocktail phage treatment (phages ΦYSZ1 + ΦYSZ2) > the polyvalent phage (ΦYSZ3 phage with broad host range) treatment > host-specific phage (ΦYSZ2 and ΦYSZ1) treatments > the control. In addition, the polyvalent phage treatment also exerted positive impact on the diversity and stability of the bacterial community in the system, suggesting that this is an environmentally friendly technique with broad applications in the biocontrol of ARPB/ARGs in soil-plant system.

Additional reduction of antibiotic resistance genes and human bacterial pathogens via thermophilic aerobic digestion of anaerobically digested sludge

Thermophilic aerobic digestion (TAD) was applied to further reduce ARGs and heavy metal resistance genes (HMRGs) as well as class 1 integrons (intI1) in sludge from anaerobic digestion (AnD). Unlike after AnD, there was no enrichment of ARGs, HMRGs and intI1 after TAD. Residual gene fractions of intI1 and total ARGs (sum of targeted ARGs) were 0.03 and 0.08, respectively. Two kinetic models (Collins-Selleck and first-order) described the decay patterns of targeted genes, revealing rapid removal of intI1 during TAD. After TAD, the relative abundance of human bacterial pathogens (HBPs) and the numbers of HBPs species decreased to approximately 68% and 64% compared to anaerobically digested sludge, respectively. Thus, TAD, subsequent to AnD, may possess high potential for reducing biological risks resulting from ARGs, HMRGs, intI1 and HBPs in sewage sludge.

Fate of antibiotic resistance genes during anaerobic digestion of sewage sludge: Role of solids retention times in different configurations

In this study, three anaerobic digestion experiments were established to investigate the effects of solids retention times (SRT) on the fate of antibiotic resistance genes (ARGs) including anaerobic digestion of sewage sludge (CK), one-stage anaerobic digestion of microwave pretreatment sludge (MW) and two-stage anaerobic digestion of microwave pretreatment sludge (Acid stage and CH₄ stage). The response of ARGs to the SRT varied significantly from ARG types and reactor configurations. Shorter SRT could avail the ARGs reduction for CK and two-stage digestion, while MW need longer SRT for the ARGs reduction. Concerning the variance of microbial community caused by reactor configurations, the role of SRT was limited. The partial redundancy analysis and structural equation models analysis indicated that the role of SRT on the ARGs fate could be attributed the most to the co-selection from heavy metals.

Hydrothermal treatment of lincomycin mycelial residues: Antibiotic resistance genes reduction and heavy metals immobilization

In this study, fate of antibiotic resistance genes (ARGs - lmrA, lmrB, ermB, lnuA, lnuB and vgaC) and species distribution of heavy metals during lincomycin mycelial residues hydrothermal treatment (HT) process were investigated. The results showed that HT could reduce both ARGs and mobile genetic elements effectively by 1.02 to 4.14 logs. Total bacterial biomass reflecting by 16S rRNA decreased from 1.27 × 10⁹ to 4.47 × 10⁵ copies g^-1 dry weight. Moreover, half-lives of these targets varied from 2.4 min (ermB) to 8.9 min (lmrB) in the first 30 min of treatment based on a biphasic first-order kinetic model. After the first 30 min, however, half-lives ranged between 15.4 min (lmrA) and 247.6 min (ISCR1). Complexation and precipitation resulted in the transformation of heavy metals from weakly bounded to relatively stable fraction in HT process. Simultaneously, their environmental risk level decreased by at least one grade.

Long-term organic fertilization increased antibiotic resistome in phyllosphere of maize

Phyllosphere contains various microorganisms that may harbor diverse antibiotic resistance genes (ARGs). However, we know little about the composition of antibiotic resistome and the factors influencing the diversity and abundance of ARGs in the phyllosphere. In this study, 16S rRNA gene amplicon sequencing and high-throughput quantitative PCR approaches were employed to investigate the effects of long-term (over 10 years) organic fertilization on the phyllosphere bacterial communities and antibiotic resistome. Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes dominated in the phyllosphere bacterial communities. Long-term application of sewage sludge and chicken manure altered the phyllosphere bacterial community composition, with a remarkable decrease in bacterial alpha-diversity. A total of 124 unique ARGs were detected in the phyllosphere. The application of sewage sludge and chicken manure significantly increased the abundance of ARGs, with a maximum 2638-fold enrichment. Variation partitioning analysis (VPA) together with network analysis indicated that the profile of ARGs is strongly correlated with bacterial community compositions. These results improve the knowledge about the diversity of plant-associated antibiotic resistome and factors influencing the profile of ARGs in the phyllosphere.

U.S. nationwide reconnaissance of ten infrequently monitored antibiotics in municipal biosolids

Ten infrequently monitored antibiotics in biosolids were examined in archived American sewage sludges (n = 79) collected as part of the 2006/2007 U.S. Environmental Protection Agency (EPA) Targeted National Sewage Sludge Survey. This study inspected the occurrence of amoxicillin, ampicillin, erythromycin, furazolidone [proxy metabolite: 3-(2-nitrobenzylidenamino)-2-oxazolidinone (NP-AOZ)], nalidixic acid, oxolinic acid, oxytetracycline, spiramycin, sulfadimidine, and sulfadimethoxine in sewage sludges after nearly a decade in frozen storage. Six antibiotics were detected at the following average concentrations (ng/g dry weight): amoxicillin (1.0), nalidixic acid (19.1), oxolinic acid (2.7), erythromycin (0.6), oxytetracycline (4.5), and ampicillin (14.8). The remaining four were not detected in any samples (<method detection limit, ng/g dry weight): sulfadimethoxine (<0.5), sulfadimidine (<1.0), spiramycin (<2.0), and NP-AOZ (<20.0). This study provides the first data on spiramycin, NP-AOZ, and nalidixic acid in U.S. sewage sludges. This study also provides new data on the losses of 5 antibiotics during long term frozen storage (-20 °C) in comparison to the 2006/2007 U.S. EPA Targeted National Sewage Sludge Survey.

Targeted inactivation of antibiotic-resistant Escherichia coli and Pseudomonas aeruginosa in a soil-lettuce system by combined polyvalent bacteriophage and biochar treatment

High abundances of antibiotic-resistant pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in agricultural soil-plant systems have become serious threats to human health and environmental safety. Therefore, it is crucial to develop targeted technology to control existing antibiotic resistance (AR) contamination and potential dissemination in soil-plant systems. In this work, polyvalent bacteriophage (phage) therapy and biochar amendment were applied separately and in combination to stimulate ARPB/ARG dissipation in a soil-lettuce system. With combined application of biochar and polyvalent phage, the abundance of Escherichia coli K-12 (tetR) and Pseudomonas aeruginosa PAO1 (ampR + fosR) and their corresponding ARGs (tetM, tetQ, tetW, ampC, and fosA) significantly decreased in the soil after 63 days' incubation (p < 0.05). Similar results for endophytic K-12 and PAO1, and ARGs, were also obtained in lettuce tissues following combined treatment. Additionally, high throughput sequencing revealed that biochar and polyvalent phage synergetically improved the structural diversity and functional stability of the indigenous bacterial communities in soil and the endophytic ones in lettuce. Hence, this work proposes a novel biotechnology that combines biochar amendment and polyvalent phage therapy to achieve targeted inactivation of ARPB, which stimulates ARG dissipation in soil-lettuce systems.