Changes in Antibiotic Resistance Gene Levels in Soil after Irrigation with Treated Wastewater: A Comparison between Heterogeneous Photocatalysis and Chlorination

Manure input propagated antibiotic resistance genes and virulence factors in soils by regulating microbial carbon metabolism

Antibiotic resistance genes (ARGs) and virulence factors (VFs) in soils represent a significant threat to ecological security and human health. The carbon-rich soil formed by manure fertilization provides an energy source for soil microbes. However, we still know little about how microbial-dominated carbon metabolism affects ARGs and VFs proliferation in soils subjected to long-term fertilization and irrigation practices in wheat-maize system. Here, we investigated soil microbial carbon metabolism, ARGs and VFs distribution, and microbial composition in soils under 9-year of different fertilization and irrigation managements during wheat growing period. Results showed that manure (M) increased total abundance of soil ARGs by 5.9 %-8.0 % and 2.1 %-4.8 % and VFs by 5.4 %-7.5 % and 2.0 %-4.9 % compared to no fertilizer (CK) and NPK fertilizer (C), respectively, regardless of irrigation. M enriched more number of ARGs and VFs types, and increased abundance of host microbes involved in carbon fixation and carbon degradation, such as Streptomyces, Lysobacter and Agromyces. M increased abundance of carbohydrate-active enzymes (CAZymes) and carbon cycle functional pathways, as well as microbial carbon metabolism capacity. Partial least squares path modeling and correlation analysis showed that microbial diversity, CAZymes, carbon cycle functional pathways (particularly carbon fixation and degradation) and microbial carbon metabolism capacity of microbial community had direct positive effects on the proliferation and spread of ARGs and VFs. In conclusion, our results highlight the importance of microbial mediated carbon metabolism in driving the dissemination of ARGs and VFs in soils under long-term manure application.

pH-gated activation of nematodes-secreted NUC-1 accelerates extracellular antibiotic resistance gene degradation in aquatic environments

The global dissemination of extracellular antibiotic resistance genes (eARGs) in environmental matrices necessitates urgent development of mitigation approaches. Although nematodes exhibit potential as biological agents for eARG degradation, significant research gaps exist in understanding their performance under diverse environmental conditions and strategies for enhancing degradation efficiency through systematic parameter optimization. Here, we systematically evaluated the degradation of plasmid-borne tetM by Caenorhabditis elegans across eight high nematodes-prevalent habitats, revealing a remarkable 38-fold variation in efficacy. Solution pH was identified as the pivotal regulatory parameter through controlled experiments. Acidification to pH 6 enhanced nematodes-mediated eARG degradation by 25-fold, effectively reducing the transformation efficiency below the detectable limit within 15 min. Through multidisciplinary analyses incorporating gene mutation analysis, mRNA quantification, capillary electrophoresis, and zymographic analysis, we demonstrate that environmental pH specifically modulates NUC-1 activity rather than expression. Structural modeling and pKa calculation reveal this pH-dependent regulation operates through protonation state change in the NUC-1 catalytic center, achieving maximal enzymatic activity at pH 6. Remarkably, this pH-gated regulatory mechanism is conserved across five nematode species spanning two distinct families, highlighting its broad biological significance and biotechnological potential. Our study establishes the first comprehensive environmental assessment framework for nematodes-mediated eARG degradation and elucidates a pH-gated regulation mechanism at the molecular level, providing a novel foundation for developing biotechnologies to control AR dissemination with spatiotemporal accuracy.

Dynamics of antibiotic resistance genes and the bacterial community after stress from a single Dazomet fumigation

Although chemical fumigants are widely applied in agriculture to control soil-borne diseases, their influence on soil antibiotic resistance genes (ARGs) remains poorly understood. This study employed metagenomic sequencing to investigate the dynamic response and recovery processes of soil bacterial communities and ARGs after the end of fumigation with Dazomet. The results revealed that the effects of Dazomet were both phased and recoverable. Initially, no significant shifts in bacterial community diversity were observed; however, by day 10 of recovery (Dazomet10), diversity had decreased by 3.1 %. By contrast, ARG levels surged by 17.3 % and 10.9 % on days 10 and 20 (Dazomet20), respectively, before reverting to the baseline by day 50 (Dazomet50). These patterns were corroborated by qPCR data, which showed a 90.8 % reduction in 16S rRNA gene abundance, alongside a 4.17- to 4.38-fold increase in the relative abundance of ARGs at Dazomet10 and Dazomet20. Approximately 63 % of the variation in ARGs was attributed to bacterial community composition and mobile genetic elements (MGEs). Combined with community analysis and host-tracking analysis, it was found that Streptomyces and Nocardioides were identified as key ARGs hosts. Overall, the microbial communities and resistome required at least 50 days after the end of fumigation to recover to their pre-fumigation state. This study sheds light on the dynamic interactions between bacterial communities and ARGs during recovery from Dazomet fumigation and underscores the critical need for the rational use of fumigants in agricultural practices.

Polyvinyl chloride microplastic triggers bidirectional transmission of antibiotic resistance genes in soil-earthworm systems

The diffusion and distribution of ubiquitous microplastics and antibiotic resistance genes (ARGs) in soil ecosystems are easily influenced by earthworm activity. However, minimal research exists on the bidirectional dissemination of ARGs in the soil-earthworm ecosystems under microplastic stress. Focusing on the typical microplastic polyvinyl chloride (PVC) microspheres in simulated soil-earthworm (Eisenia fetida) systems, we characterized the PVC-triggered interactive transmission of ARGs between earthworm guts and their dwelling soils using shotgun metagenomics and qPCR methodologies. PVC exposure did not alter the diversity and relative abundance of ARGs in earthworm-uninoculated soils but significantly increased those in earthworm-inoculated soils. Meanwhile, the abundance of ARGs increased in the earthworm gut under PVC stress. Source tracking analysis showed a higher source proportion of soil-borne ARGs into earthworm gut under PVC treatments. Mechanistically, PVC-triggered increasing prevalence of ARGs was significantly related to both the bacterial community and mobile genetic elements-mediated horizontal transfer in the soils, whereas the bacterial community predominated the process in the earthworm guts. Overall, our findings reveal a PVC-triggered bidirectional transmission pattern of ARGs between earthworm guts and their dwelling soils and highlight the overlooked ecotoxicological risk of microplastics in soil-earthworm systems.

Degradation of extracellular antibiotic resistance gene through singlet oxygen produced by carbon nanotubes-activated persulfate

Extracellular antibiotic resistance gene (eARG) has emerged as a global crisis in recent years, yet commonly used disinfectants have proven ineffective for their elimination. Seeking to enhance the degradation efficiency of eARG, this study explored the potential of carbon nanotubes-activated persulfate (CNTs + PS) system as a novel method for eradicating eARG. Our findings demonstrated that CNTs + PS effectively disrupted the intact structure of eARG, inhibited their genetic replication and horizontal transfer capability, achieving remarkable degradation of eARG contamination. Further experiments revealed that 1O2 played a predominant role in eARG degradation, while electron transfer played minor roles in the degradation process. The carbonyl groups served as the primary sites for activating PS to generate 1O2. CNTs can enhance the efficiency of electron transfer from eARG to PS. Moreover, the degradation efficacy of eARG by CNTs + PS was influenced by various factors including the dosage ratio between CNTs and PS, initial concentrations of eARG, pH values, inorganic anions and humic substances and water matrix. Reusability experiment demonstrated that CNTs + PS exhibited stable degradation performance after multiple uses. These findings offer a new perspective for the efficient degradation of eARG in environmental remediation.

Effective inhibition of chloride ion interference in photocatalytic process by negatively charged molecularly imprinted photocatalyst: Behavior and mechanism

The ubiquitous chloride ions (Cl-) in water seriously interfere with pollutant oxidation and inevitably generate undesirable chlorinated byproducts. In this study, we report for the first time that a negatively charged molecularly imprinted photocatalyst (MIP) can effectively inhibit Cl- interference and suppress the production of chlorination byproducts (the yield of chloroacetic acid was only 16 % of the bare photocatalyst system) while ensuring efficient degradation of target pollutants, thereby greatly improving the safety of the pollutant degradation process. Taking antibiotics as target pollutant, we investigated the mechanism of action of MIP by comparing the antibiotic degradation pathways, fate of photogenerated active species and production of reactive chlorine species (RCS) in the MIP and bare photocatalyst system. The mechanism by which MIP inhibits Cl- interference was mainly based on a synergy between electrostatic repulsion and steric hindrance induced by the specific capture of antibiotics in imprinted cavity, which effectively suppressed the production of RCS and hindered the participation of RCS in antibiotics degradation. In addition, MIP showed good compatibility with common cations, anions and organic matter, and performed well within a broad pH range in various water environments. Thus, the negatively charged MIP provides a feasible approach for the safe and efficient removal of pollutants in Cl- containing water.

An in-depth study of integrating cascaded photocatalytic H2O2 generation and activation with solar-driven interfacial evaporation for in-situ organic contaminant remediation

Integrating cascaded photocatalytic H2O2 generation and subsequent activation of H2O2 (into ·OH radicals) with solar-driven interfacial evaporation techniques offers an effective and sustainable approach for in-situ treating water contaminated with organic substances. Unlike traditional water-dispersed catalysts, the interfacial evaporation approach presents unique challenges in photocatalytic reactions. We explored these dynamics using an AgI/PPy/MF interfacial photothermal set, achieving H2O2 production efficiency (approximately 1.53 mM/g/h) - three times higher than submerged counterparts. This efficiency is attributed to exceptional solar light absorption (about 95 %), a significant surface photothermal effect (raising temperatures by approximately 36 °C), and enhanced oxygen availability (38 times more than in water), all characteristic of the interfacial system. The in-situ activation of H2O2 into ·OH notably improves the degradation of organic pollutants, achieving up to 99 % removal efficiency. This comprehensive analysis highlights the potential of combining photocatalytic H2O2 processes with interfacial evaporation for efficiently purifying organically polluted water.

Impacts of irrigation with treated livestock wastewater on the accumulation characteristic of ARGs in the farmland soil: a case study in Hohhot, China

Irrigation with treated livestock wastewater (TWW) is a promising strategy for reusing resources. However, TWW irrigation might introduce antibiotic resistant genes (ARGs) into the soil, posing environmental risks associated with antibiotic resistance. This study focuses on investigating the influence of irrigation amounts and duration on the fate of ARGs and identifies key factors driving their changes. The results showed that there were 13 ARGs in TWW, while only 5 ARGs were detected in irrigated soil. That is some introduced ARGs from TWW could not persistently exist in the soil. After 1-year irrigation, an increase in irrigation amount from 0.016 t/m2 to 0.048 t/m2 significantly enhanced the abundance of tetC by 29.81%, while ermB and sul2 decreased by 45.37% and 76.47%, respectively (p < 0.01). After 2-year irrigation, the abundance of tetC, ermB, ermF, dfrA1, and total ARGs significantly increased (p < 0.05) when the irrigation amount increased. The abundances of ARGs after 2-year irrigation were found to be 2.5-34.4 times higher than 1 year. Obviously, the irrigation years intensified the positive correlation between ARGs abundance and irrigation amount. TetC and ermF were the dominant genes resulting in the accumulation of ARGs. TWW irrigation increased the content of organic matter and total nitrogen in the soil, which affected microbial community structure. The changes of the potential host were the determining factors driving the ARGs abundance. Our study demonstrated that continuous TWW irrigation for 2 years led to a substantial accumulation of ARGs in soil.

Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress

Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.

Investigating the effects of irrigation with indirectly recharged groundwater using recycled water on soil and crops in semi-arid areas

The utilization of direct wastewater for irrigation poses many environmental problems such as soil quality deterioration due to the accumulation of salts, heavy metals, micro-pollutants, and health risks due to undesirable microorganisms. This hampers its agricultural reuse in arid and semi-arid regions. To address these concerns, the present study introduces a recent approach that involves using indirectly recharged groundwater (GW) with secondary treated municipal wastewater (STW) for irrigation through a Soil Aquifer Treatment-based system (SAT). This method aims to mitigate freshwater scarcity in semi-arid regions. The study assessed GW levels, physicochemical properties, and microbial diversity of GW, and soil in both impacted (receiving recycled water) and non-impacted (not receiving recycled water) areas, before recycling (2015-2018) and after recycling (2019-2022) period of the project. The results indicated a significant increase of 68-70% in GW levels of the studied boreholes in the impacted areas. Additionally, the quality of indirectly recharged GW in the impacted areas improved notably in terms of electrical conductivity (EC), hardness, total dissolved solids (TDS), sodium adsorption ratio (SAR), along with certain cations and anions (hard water to soft water). No significant difference was observed in soil properties and microbial diversity of the impacted areas, except for EC and SAR, which were reduced by 50% and 39%, respectively, after the project commenced. The study also monitored specific microbial species, including total coliforms, Escherichia coli (as indicator organisms), Shigella, and Klebsiella in some of the harvested crops (beetroot, tomato, and spinach). However, none of the analysed crops exhibited the presence of the studied microorganisms. Overall, the study concludes that indirectly recharged GW using STW is a better sustainable and safe irrigation alternative compared to direct wastewater use or extracted hard GW from deep aquifers.

Simultaneous removal of antibiotics and antibiotic resistant genes using a CeO2@CNT electrochemical membrane-NaClO system

The simultaneous removal of antibiotic and antibiotic resistance genes (ARGs) are important to inhibit the spread of antibiotic resistance. In this study, a coupled treatment system was developed using a CeO2 modified carbon nanotube electrochemical membrane and NaClO (denoted as CeO2@CNT-NaClO) to treat simulated water samples containing antibiotics and antibiotic-resistant bacteria (ARB). As the mass ratio of CeO2 to CNT was 5:7 and the current density was 2.0 mA/cm2, the CeO2@CNT-NaClO system removed 99% of sulfamethoxazole, 4.6 log sul1 genes, and 4.7 log intI1 genes from the sulfonamide-resistance water samples, and removed 98% of tetracycline, 2.0 log tetA genes, and 2.6 log intI1 genes of the tetracycline-resistance water samples. The outstanding performance of the CeO2@CNT-NaClO system for simultaneously removing antibiotic and ARGs was mainly ascribed to the generation of multiple reactive species, including •OH, •ClO, •O2- and 1O2. Antibiotics can undergo efficient degradation by •OH. However, the reaction between •OH and antibiotics reduces the availability of •OH to permeate into the cells and react with DNA. Nevertheless, the presence of •OH enhancd the effects of •ClO, •O2-, and 1O on ARG degradation. Through the coupled action of •OH, •ClO, •O2-, and 1O2, the cell membranes of ARB experience severe damage, resulting in an increase in intracellular reactive oxygen species (ROS) and a decrease in superoxide dismutase (SOD) activity. Consequently, this coordinated mechanism leads to superior removal of ARGs.

Efficient Degradation of Intracellular Antibiotic Resistance Genes by Photosensitized Erythrosine-Produced 1O2

Intracellular antibiotic resistance genes (iARGs) constitute the important part of wastewater ARGs and need to be efficiently removed. However, due to the dual protection of intracellular DNA by bacterial membranes and the cytoplasm, present disinfection technologies are largely inefficient in iARG degradation. Herein, we for the first time found that erythrosine (ERY, an edible dye) could efficiently degrade iARGs by producing abundant 1O2 under visible light. Seven log antibiotic-resistant bacteria were inactivated within only 1.5 min, and 6 log iARGs were completely degraded within 40 min by photosensitized ERY (5.0 mg/L). A linear relationship was established between ARG degradation rate constants and 1O2 concentrations in the ERY photosensitizing system. Surprisingly, a 3.2-fold faster degradation of iARGs than extracellular ARGs was observed, which was attributed to the unique indirect oxidation of iARGs induced by 1O2. Furthermore, ERY photosensitizing was effective for iARG degradation in real wastewater and other photosensitizers (including Rose Bengal and Phloxine B) of high 1O2 yields could also achieve efficient iARG degradation. The findings increase our knowledge of the iARG degradation preference by 1O2 and provide a new strategy of developing technologies with high 1O2 yield, like ERY photosensitizing, for efficient iARG removal.

Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples

Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.

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.

Exposure Levels of Airborne Fungi, Bacteria, and Antibiotic Resistance Genes in Cotton Farms during Cotton Harvesting and Evaluations of N95 Respirators against These Bioaerosols

The USA is the third-leading cotton-producing country worldwide and cotton farming is common in the state of Georgia. Cotton harvest can be a significant contributor to airborne microbial exposures to farmers and nearby rural communities. The use of respirators or masks is one of the viable options for reducing organic dust and bioaerosol exposures among farmers. Unfortunately, the OSHA Respiratory Protection Standard (29 CFR Part 1910.134) does not apply to agricultural workplaces and the filtration efficiency of N95 respirators was never field-tested against airborne microorganisms and antibiotic resistance genes (ARGs) during cotton harvesting. This study addressed these two information gaps. Airborne culturable microorganisms were sampled using an SAS Super 100 Air Sampler in three cotton farms during cotton harvesting, and colonies were counted and converted to airborne concentrations. Genomic DNA was extracted from air samples using a PowerSoil^® DNA Isolation Kit. A series of comparative critical threshold (2^-ΔΔCT) real-time PCR was used to quantify targeted bacterial (16S rRNA) genes and major ARGs. Two N95 facepiece respirator models (cup-shaped and pleated) were evaluated for their protection against culturable bacteria and fungi, total microbial load in terms of surface ATP levels, and ARGs using a field experimental setup. Overall, culturable microbial exposure levels ranged between 10³ and 10⁴ CFU/m³ during cotton harvesting, which was lower when compared with bioaerosol loads reported earlier during other types of grain harvesting. The findings suggested that cotton harvesting works can release antibiotic resistance genes in farm air and the highest abundance was observed for phenicol. Field experimental data suggested that tested N95 respirators did not provide desirable >95% protections against culturable microorganisms, the total microbial load, and ARGs during cotton harvesting.

Degradation of Antibiotic Resistance Genes by VADER with CRISPR-Cas Immunity

The evolution and dissemination of antibiotic resistance genes (ARGs) are prompting severe health and environmental issues. While environmental processes, e.g., biological wastewater treatment, are key barriers to prevent the spread of ARGs, they are often sources of ARGs at the same time, requiring upgraded biotechnology. Here, we present VADER, a synthetic biology system for the degradation of ARGs based on CRISPR-Cas immunity, an archaeal and bacterial immune system for eliminating invading foreign DNAs, to be implemented for wastewater treatment processes. Navigated by programmable guide RNAs, VADER targets and degrades ARGs depending on their DNA sequences, and by employing an artificial conjugation machinery, IncP, it can be delivered via conjugation. The system was evaluated by degrading plasmid-borne ARGs in Escherichia coli and further demonstrated via the elimination of ARGs on the environmentally relevant RP4 plasmid in Pseudomonas aeruginosa. Next, a prototype conjugation reactor at a 10-mL scale was devised, and 100% of the target ARG was eliminated in the transconjugants receiving VADER, giving a proof of principle for the implementation of VADER in bioprocesses. By generating a nexus of synthetic biology and environmental biotechnology, we believe that our work is not only an enterprise for tackling ARG problems but also a potential solution for managing undesired genetic materials in general in the future. IMPORTANCE Antibiotic resistance has been causing severe health problems and has led to millions of deaths in recent years. Environmental processes, especially those of the wastewater treatment sector, are an important barrier to the spread of antibiotic resistance from the pharmaceutical industry, hospitals, or civil sewage. However, they have been identified as a nonnegligible source of antibiotic resistance at the same time, as antibiotic resistance with its main cause, antibiotic resistance genes (ARGs), may accumulate in biological treatment units. Here, we transplanted the CRISPR-Cas system, an immune system via programmable DNA cleavage, to tackle the antibiotic resistance problem raised in wastewater treatment processes, and we propose a new sector specialized in ARG removal with a conjugation reactor to implement the CRISPR-Cas system. Our study provides a new angle for resolving public health issues via the implementation of synthetic biology in environmental contexts at the process level.

Hormetic Effect of Pyroligneous Acids on Conjugative Transfer of Plasmid-mediated Multi-antibiotic Resistance Genes within Bacterial Genus

Spread of antibiotic resistance genes (ARGs) by conjugation poses great challenges to public health. Application of pyroligneous acids (PA) as soil amendments has been evidenced as a practical strategy to remediate pollution of ARGs in soils. However, little is known about PA effects on horizontal gene transfer (HGT) of ARGs by conjugation. This study investigated the effects of a woody waste-derived PA prepared at 450°C and its three distillation components (F1, F2, and F3) at different temperatures (98, 130, and 220°C) on conjugative transfer of plasmid RP4 within Escherichia coli. PA at relatively high amount (40-100 μL) in a 30-mL mating system inhibited conjugation by 74-85%, following an order of PA > F3 ≈ F2 ≈ F1, proving the hypothesis that PA amendments may mitigate soil ARG pollution by inhibiting HGT. The bacteriostasis caused by antibacterial components of PA, including acids, phenols, and alcohols, as well as its acidity (pH 2.81) contributed to the inhibited conjugation. However, a relatively low amount (10-20 μL) of PA in the same mating system enhanced ARG transfer by 26-47%, following an order of PA > F3 ≈ F2 > F1. The opposite effect at low amount is mainly attributed to the increased intracellular reactive oxygen species production, enhanced cell membrane permeability, increased extracellular polymeric substance contents, and reduced cell surface charge. Our findings highlight the hormesis (low-amount promotion and high-amount inhibition) of PA amendments on ARG conjugation and provide evidence for selecting an appropriate amount of PA amendment to control the dissemination of soil ARGs. Moreover, the promoted conjugation also triggers questions regarding the potential risks of soil amendments (e.g., PA) in the spread of ARGs via HGT.

Chlorination (but Not UV Disinfection) Generates Cell Debris that Increases Extracellular Antibiotic Resistance Gene Transfer via Proximal Adsorption to Recipients and Upregulated Transformation Genes

To advance the understanding of antibiotic resistance propagation from wastewater treatment plants, it is important to elucidate how different effluent disinfection processes affect the dissemination of predominantly extracellular antibiotic resistance genes (eARGs). Here, we show that, by facilitating proximal adsorption to recipient cells, bacterial debris generated by chlorination (but not by UV irradiation) increases the natural transformation frequency of their adsorbed eARG by 2.9 to 7.2-fold relative to free eARGs. This is because chlorination increases the bacterial surface roughness by 1.1 to 6.7-fold and the affinity toward eARGs by 1.6 to 5.8-fold, and 98% of the total eARGs released after chlorination were adsorbed to cell debris. In contrast, UV irradiation released predominantly free eARGs with 18% to 56% lower transformation frequency. The collision theory indicates that the ARG donor-recipient collision frequency increased by 35.1-fold for eARGs adsorbed onto chlorination-generated bacterial debris, and the xDLVO model infers a 29% lower donor-recipient contact energy barrier for these ARGs. Exposure to chlorination-generated bacterial debris also upregulated genes associated with natural transformation in Vibrio vulnificus (e.g., tfoX encoding the major activator of natural transformation) by 2.6 to 5.2-fold, likely due to the generation of chlorinated molecules (5.1-fold higher Cl content after chlorination) and persistent reactive species (e.g., carbon-centered radicals) on bacterial debris. Increased proximal eARG adsorption to bacterial debris was also observed in the secondary effluent after chlorination; this decreased eARG decay by 64% and increased the relative abundance of ARGs by 7.2-fold. Overall, this study highlights that different disinfection approaches can result in different physical states of eARGs that affect their resulting dissemination potential via transformation.

Antibiotic resistance genes and bacterial diversity: A comparative molecular study of treated sewage from different origins and their impact on irrigated soils

Present study aims to investigate how is soil affected following irrigation with treated effluents of different origins by analysing the bacterial diversity, metabolic diversity and antibiotic resistance genes (ARGs). Comparative analysis with previously reported ARGs in effluents was performed to understand the mobility of ARGs from treated wastewater to the irrigated soil with respect to the control soil regimen. Acinetobacter, Burkholderia and Pseudomonas were observed as the most abundant genera in all the samples. The metabolic gene abundance of all the samples suggests a prominent contribution to natural mineral recycling. Most abundant ARGs observed encode resistance for clindamycin, kanamycin A, macrolides, paromomycin, spectinomycin and tetracycline. Treated effluent reuse did not appear to enhance the ARG levels in soils in most cases except for institutional treatment site (M), where the ARGs for aminoglycosides, β-lactams and sulfonamides were found to be abundantly present in both treated effluent and the irrigated soil. This study finds the importance of wastewater treatment from different origins and the impact of treated wastewater reuse in irrigation. This study also emphasises on the better understanding of ARGs mobility from water to soil.

Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics

Antimicrobial resistance (AMR) in soils represents a serious risk to human health through the food chain and human-nature contact. However, the active antibiotic-resistant bacteria (ARB) residing in soils that primarily drive AMR dissemination are poorly explored. Here, single-cell Raman-D₂O coupled with targeted metagenomics is developed as a culture-independent approach to phenotypically and genotypically profiling active ARB against clinical antibiotics in a wide range of soils. This method quantifies the prevalence (contamination degree) and activity (spread potential) of soil ARB and reveals a clear elevation with increasing anthropogenic activities such as farming and the creation of pollution, thereby constituting a factor that is critical for the assessment of AMR risks. Further targeted sorting and metagenomic sequencing of the most active soil ARB uncover several uncultured genera and a pathogenic strain. Furthermore, the underlying resistance genes, virulence factor genes, and associated mobile genetic elements (including plasmids, insertion sequences, and prophages) are fully deciphered at the single-cell level. This study advances our understanding of the soil active AMR repertoire by linking the resistant phenome to the genome. It will aid in the risk assessment of environmental AMR and guide the combat under the One Health framework.

Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal

Antibiotic-resistant bacteria-associated infections are responsible for more than 1.2 million annual deaths worldwide. In low- and middle-income countries (LMICs), the consumption of antibiotics for human and veterinary uses is not regulated effectively. Overused and misused antibiotics can end up in aquatic environments, which may act as a conduit for antibiotic resistance dissemination. However, data on the prevalence of antibiotic resistance determinants in aquatic environments are still limited for LMICs. In this study, we evaluated the prevalence and concentration of antibiotic resistance genes (ARGs) in different drinking and environmental water sources collected from the Kathmandu Valley, Nepal, using droplet digital polymerase chain reaction to understand the current situation of ARG contamination. River water and shallow dug well water sources were the most contaminated with ARGs. Almost all samples contained sul1 (94%), and intI1 and tet(A) were detected in 83 and 60% of the samples, respectively. Maximum ARG concentration varied between 4.2 log₁₀ copies/100 ml for mecA and 9.3 log₁₀ copies/100 ml for sul1. Significant positive correlations were found between ARGs (r > 0.5, p < 0.01), except for mecA, qnrS, and vanA. As sul1 and intI1 were detected in almost all samples, the presence of these genes in a given sample may need to be considered as background antibiotic resistance in LMICs. Therefore, monitoring of ARGs, such as β-lactam ARGs, quinolone resistance genes, and vancomycin resistance genes, may provide a better picture of the antibiotic resistance determinants in aquatic environments of LMICs.

Application of α-Fe2O3 nanoparticles in controlling antibiotic resistance gene transport and interception in porous media

Metal oxide nanoparticles (MONPs) with a large specific surface area are expected to bind with antibiotic resistance genes (ARGs), thereby controlling ARGs' contamination by reducing their concentration and mobilization. Here, adsorption experiments were carried out and it was found that α-Fe₂O₃ NPs could chemically bind with ARGs (tetM-carrying plasmids) in water with an adsorption rate of 0.04 min^-1 and an adsorption capacity of 7.88 g/kg. Mixing α-Fe₂O₃ NPs into quartz sand column markedly increased the interceptive removal of ARGs from inflow water. The interception rate of 1.0 μg/mL ARGs in ultrapure water (25 mL, 5 pore volumes) through the sand column (plexiglass, length 8 cm, internal diameter 1.4 cm) with 1 g/kg α-Fe₂O₃ NPs was 1.73 times of that through the pure sand column; the interception rate overall increased with increasing addition of α-Fe₂O₃ NPs, reaching 68.8% with 20 g/kg α-Fe₂O₃ NPs. Coexisting Na⁺ (20 mM), Ca²⁺ (20 mM), and acidic condition (pH 4.0) could further increase the interception rate of ARGs by 1 g/kg α-Fe₂O₃ NPs from 21.1% to 86.2%, 90.7%, and 96.2%, respectively. The presence of PO₄^3- and humic acid at environmentally relevant concentrations would not significantly affect the interception of ARGs. In the treatment groups with PO₄^3- and humic acid, the removal rate decreased by only 1.8% and 0.1%, respectively. In addition, the interceptive removal of ARGs by α-Fe₂O₃ NPs-incorporated sand column was even better in actual surface water samples (87.2%) than that in the ultrapure water (21.1%). The findings provide a promising approach to treat ARGs-polluted water.

Antibiotic resistance in soil and tomato crop irrigated with freshwater and two types of treated wastewater

Agricultural use of treated wastewater (TWW) is an effective means to reduce freshwater (FW) consumption. However, there is a growing concern regarding the potential dissemination of antibiotic resistance elements by TWW irrigation. We hypothesized that higher levels of antibiotic resistance genes (ARGs) would be detected in soil and crops irrigated with TWW compared to FW irrigation. To test our prediction, samples of water (FW, secondary TWW, and tertiary TWW), irrigated soils, and crops (tomato) surface wash were collected during two consecutive growing seasons. The ARGs conferring resistance to sulfonamide, fluoroquinolone, penicillin, erythromycin and tetracycline were quantified in the samples, alongside Class 1 integron-integrase and the bacterial 16 S rRNA encoding genes. Contrary to our hypothesis, ARGs in the irrigation water were not propagated to either the irrigated soil, or the tomato. The tomato surface wash featured a variety of ARGs that were undetected in neither the waters nor the irrigated soils. Therefore, we cautiously question the link between irrigation water quality and the soil and produce resistomes.

Fate of antibiotic resistant genes in wastewater environments and treatment strategies - A review

Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) have emerged in aquatic environments through the discharge of large amounts of antibiotics into wastewater. Well-designed wastewater treatment plants (WWTPs) with effective treatment processes are essential to prevent the release of ARGs directly into the environment. Although some systematic sequential treatment methods are used to remove ARGs, considerable gaps in removal mechanisms will be discussed. Therefore, deep analysis and discussion of various treatment methods are required to understand the ARGs removal mechanisms. In this manuscript, the role of antibiotics and the resistance mechanism of ARB are discussed in depth. In addition, the fate of ARGs in an aquatic environment and detection methods are compared comprehensively and discussed. In particular, the advantages and disadvantages of various methods are summarized and reviewed critically. Finally, combined technologies, such as advanced oxidation process (AOP) with biochemical systems, membrane separation with electrochemical AOP, ultrafiltration (UF) membrane coupled with photocatalytic treatment, and UF membrane separation coupled with sonication, are introduced. Overall, low-energy anaerobic treatment reactors with any of the above combined treatments might reduce the discharge of large quantities of ARGs into the environment. Finally, this review provides valuable insights for better ARG removal technologies by introducing combined effective treatment strategies used in real WWTPs.

Regrowth of Escherichia coli in environmental waters after chlorine disinfection: shifts in viability and culturability

Bacterial regrowth after water/wastewater disinfection poses severe risks to public health. However, regrowth studies under realistic water conditions that might critically affect bacterial regrowth are scarce. This study aimed to assess for the first time the regrowth of Escherichia coli (E. coli) in terms of its viability and culturability in environmental waters after chlorine disinfection, which is the most widely used disinfection method. Post-chlorination regrowth tests were conducted in 1) standard 0.85% NaCl solution, 2) river water receiving domestic wastewater effluents, and 3) river water that is fully recharged by domestic wastewater effluents. The multiplex detection of plate count and fluorescence-based viability test was adopted to quantify the culturable and viable E. coli to monitor the regrowth process. The results confirmed that chlorine treatment (0.2, 0.5 and 1.0 mg L-1 initial free chlorine) induced more than 99.95% of E. coli to enter a viable but non-culturable (VBNC) state and the reactivation of VBNC E. coli is presumably the major process of the regrowth. A second-order regrowth model well described the temporal shift of the survival ratio of culturable E. coli after the chlorination (R2: 0.73-1.00). The model application also revealed that the increase in initial chlorine concentration and chlorine dose limited the maximum regrowth rate and the maximum survival ratio, and the regrowth rate and percentage also changed with the water type. This study gives a better understanding of the potential regrowth after chlorine disinfection and highlights the need for investigating the detailed relation of the regrowth to environmental conditions such as major components of water matrices.

Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones

The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.

The dissemination of antibiotics and their corresponding resistance genes in treated effluent-soil-crops continuum, and the effect of barriers

Irrigation with treated effluent is expanding as freshwater sources diminish, but hampered by growing concerns of pharmaceuticals contamination, specifically antibiotics and resistance determinants. To evaluate this concern, freshwater and effluent were applied to an open field that was treated with soil barriers including plastic mulch together with surface and subsurface drip irrigation, cultivating freshly eaten crops (cucumbers or melons) for two consecutive growing seasons. We hypothesized that the effluent carries antibiotics and resistance determinants to the drip-irrigated soil and crops regardless of the treatment. To test our hypothesis, we monitored for antibiotics abundance (erythromycin, sulfamethoxazole, tetracycline, chlortetracycline, oxytetracycline, amoxicillin, and ofloxacin) and their corresponding resistance genes (ermB, ermF, sul1, tetW, tetO, bla_TEM and qnrB), together with class 1 integron (intl1), and bacterial 16S rRNA, in water, soil, and crop samples taken over two years of cultivation. The results showed that an array of antibiotics and their corresponding resistance genes were detected in the effluent but not the freshwater. Yet, there were no significant differences in the distribution or abundance of antibiotics and resistance genes, regardless of the irrigation water quality, or crop type (p > 0.05), but plastic-covered soil irrigated with effluent retained the antibiotics oxytetracycline and ofloxacin (p < 0.05). However, we could not detect significant correlations between the detected antibiotics and the corresponding resistance genes. Overall, our findings disproved our hypothesis suggesting that treated effluent may not carry antibiotics resistance genes to the irrigated soil and crops yet, plastic mulch covered soil retain some antibiotics that may inflict long term contamination.

Distribution characteristics of antibiotic resistance bacteria and related genes in urban recreational lakes replenished by different supplementary water source

The distribution characteristics of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in urban recreational water from different water-supply sources might be different. In this study, water samples were collected to detect the antibiotic resistance of heterotrophic bacteria to five antibiotics, and the content, phenotype, gene type and species distribution of resistant bacteria were analyzed. The results showed that the changes of bacteria resistance rate in two lakes to five kinds of antibiotics were synchronous with time, and it would reach its maximum in autumn. The detection of ARGs and int I in 80 resistance strains showed that the detection rate of tetG, tetA and int I was high. Here, 51.25% of the bacteria were doubly resistant to AMP-CTX. The 80 isolate strains were of nine genera and 19 species, among which Bacillus cereus, Escherichia coli, Aeromonas veronii, Aeromonas caviae and Raoultella ornithinolytica were the common ARB species in two lakes. Correlation analysis showed that the water temperature was significantly correlated with the content of ARB in sulfamethoxazole (SMZ) and cefotaxime (CTX) (p < 0.05), and the total phosphorus (TP) in FQ lake was significantly correlated with the content of AMP-resistant bacteria (p < 0.05), while there were no other correlations between the changes of other water quality indexes and the content of ARB (p > 0.05).

Spinning disc photoreactor based visible-light-driven Ag/Ag2O/TiO2 heterojunction photocatalyst film toward the degradation of amoxicillin

The presence of antibiotics in waste and drinking water is causing increasing concern around the world, thereby an advanced sustainable technology needs to be developed to eliminate the antibiotics from water resources. Hence, an efficient spinning disc photoreactor (SDPR) equipped with visible light-activated Ag/Ag₂O/TiO₂ heterostructure thin film photocatalyst was assessed for the degradation of amoxicillin (AMX) as a typical antibiotic. The surface morphology, optoelectronic and structural features of Ag/Ag₂O/TiO₂ heterojunction were characterized by TEM, BET, mott Schottky, FESEM, EDS, AFM, XRD, UV-Vis-DRS, and contact angle measurements. Results confirm that Ag and Ag₂O have a significant effect on the photocharge carrier separation and transfer of the as-developed photocatalyst system. The operative variables including illumination time, rotational speed, solution flow rate, aeration rate, pH, and initial AMX concentration were optimized by CCD. The results displayed the maximum AMX photodegradation (97.91%) could be achieved at optimal conditions involving illumination time of 80 min, a rotational speed of 225 rpm, the solution flow rate of 0.6 L/min, aeration rate of 20 L/min, pH = 6, and initial AMX concentration of 20 mg/L. Interestingly, more than 79% COD and 64% TOC were removed under optimum conditions during 80 min illumination time, respectively. Active species tests confirmed the dominant role of ·OH and ·O₂^- in AMX degradation. finally, the XRD pattern confirmed that the reusability assessments of the heterojunction film could successfully retain its stability for six consecutive photocatalytic degradation runs. This work demonstrates the feasibility of utilizing visible-light-driven thin-film photocatalysts in spinning disc photoreactors in treating the tenacious antibiotic pollutants.

Individual and combined applications of biochar and pyroligneous acid mitigate dissemination of antibiotic resistance genes in agricultural soil

Remediation of agricultural soils polluted with antibiotic resistance genes (ARGs) is important for protecting food safety and human health. However, the feasibility of co-application of biochar and pyroligneous acid, two multifunctional soil amendments, for mitigating dissemination of soil ARGs is unknown. Thus, a woody biochar (BC450) and its by-product, pyroligneous acid (PA450) simultaneously produced at 450 °C from blended wood wastes, were used to compare their individual and combined effects on soil ARG abundance using a 65-day pot experiment planted with leafy vegetable Brassica chinensis L. The individual and combined applications of PA450 and BC450 significantly reduced the absolute abundance of ARGs by 65.7-81.4% and 47.5-72.9% in the corresponding rhizosphere and bulk soil. However, the co-application showed little synergistic effect, probably due to the counteractive effect of BC450 on the PA450-mitigated soil ARG proliferation, resulted from the promoted soil bacterial growth and/or adsorption of antimicrobial components of PA450 by BC450. The decreased abundances of mobile genetic element intI1 and Tn916/1545 in the PA450 treatments demonstrated the potential of PA450 for weakening horizontal gene transfer (HGT). Furthermore, weakened HGT by individual PA450, lowered availability of heavy metals by individual BC450, and different bacterial community (e.g., reduced ARGs bacterial host) together with improved soil properties from co-application of PA450 and BC450 all contributed to the reduced ARG level. This study highlighted the feasibility of co-applications of biochar and pyroligneous acid amendment for mitigating soil ARG pollution. These findings provide important information for developing eco-friendly technologies using biochar and pyroligneous acid in remediating ARG-contaminated soils.

Antibiotic resistance and class 1 integron genes distribution in irrigation water-soil-crop continuum as a function of irrigation water sources

The increasing demand for fresh water coupled with the need to recycle water and nutrients has witnessed a global increase in wastewater irrigation. However, the development of antibiotic resistance hotspots in different environmental compartments, as a result of wastewater reuse is becoming a global health concern. The effect of irrigation water sources (wastewater, surface water, fresh water) on the presence and abundance of antibiotic resistance genes (ARGs) (bla_CTX-m-32, tet-W, sul1, cml-A, and erm-B) and class 1 integrons (intI1) were investigated in the irrigation water-soil-crop continuum using quantitative real-time PCR (qPCR). Sul1 and bla_CTX-m-32 were the most and least abundant ARGs in three environments, respectively. The abundance of ARGs and intI1 significantly decreased from wastewater to surface water and then fresh water. However, irrigation water sources had no significant effect on the abundance of ARGs and intI1 in soil and crop samples. Principal component analysis (PCA) showed that UV index and air temperature attenuate the abundance of ARGs and intI1 in crop samples whereas the air humidity and soil electrical conductivity (EC) promotes the ARGs and intI1. So that the climate condition of semi-arid regions significantly affects the abundance of ARGs and intI1 in crop samples. The results suggest that treated wastewater might be safely reused in agricultural practice in semi-arid regions without a significant increase of potential health risks associated with ARGs transfer to the food chain. However, further research is needed for understanding and managing ARGs transfer from the agricultural ecosystem to humans through the food chain.

Abundance and Dynamic Distribution of Antibiotic Resistance Genes in the Environment Surrounding a Veterinary Antibiotic Manufacturing Site

Background: Antibiotics releasing from the manufacturing sites to the surrounding environment has been identified as a risk factor for the development of antibiotic resistance of bacterial pathogens. However, the knowledge of the abundance and distribution of antibiotic resistance genes (ARGs) influenced by antibiotic pollution is still limited. Methods: In this work, the contamination by resistance genes of the environmental media including an urban river and soil along the river located near the sewage outlet of a veterinary antibiotic manufacturing site in Shijiazhuang, China, was assessed. The abundance and dynamic distribution of ARGs in different sampling points and during different seasons were analyzed using fluorescent quantitative PCR method (qPCR). Results: A total of 11 resistance genes, one integron and one transposon were detected in water and soils around the pharmaceutical factory, and among which, the sulfonamide resistance genes sul1 and β-lactam resistance genes blaSHV were the most abundant genes. The relative abundance of ARGs in both river water and soil samples collected at the downstream of the sewage outlet was higher than that of samples collected at the upstream, non-polluted areas (p < 0.05). The mobile genetic elements (MGEs) integron in river was significantly correlated (p < 0.05) with the relative abundance of ARGs. Conclusions: The results indicate that the discharge of waste from antibiotic manufacturing site may pose a risk of horizontal transfer of ARGs.

Irreversible inactivation of carbapenem-resistant Klebsiella pneumoniae and its genes in water by photo-electro-oxidation and photo-electro-Fenton - Processes action modes

Carbapenem-resistant Klebsiella pneumoniae is a critical priority pathogen according to the World Health Organization's classification. Effluents of municipal wastewater treatment plants (EWWTP) may be a route for K. pneumoniae dissemination. Herein, the inactivation of this microorganism in simulated EWWTP by the photo-electro-oxidation (PEO) and photo-electro-Fenton (PEF) processes was evaluated. Firstly, the disinfecting ability and action pathways of these processes were established. PEO achieved faster K. pneumoniae inactivation (6 log units in 75 min of treatment) than the PEF process (6 log units in 105 min of treatment). PEO completely inactivated K. pneumoniae due to the simultaneous action of UVA light, electrogenerated H₂O_2, and anodic oxidation pathways. The slower inactivation of K. pneumoniae when using PEF was related to interfering screen effects of iron oxides on light penetration and the diffusion of the bacteria to the anode. However, both PEO and PEF avoided the recovery and regrowth of treated bacteria (with no detectable increase in the bacteria concentration after 24 h of incubation). In addition to the bacteria evolution, the effect of treatment processes on the resistance gene was examined. Despite inactivation of K. pneumoniae by PEF was slower than by PEO, the former process induced a stronger degrading action on the gene, conferring the resistance to carbapenems (PEF had a Ct value of 24.92 cycles after 105 min of treatment, while PEO presented a Ct of 19.97 cycles after 75 min). The results of this research indicate that electrochemical processes such as PEO and PEF are highly effective at dealing with resistant K. pneumoniae in the EWWTP matrix.

Metagenomics analysis reveals the distribution and communication of antibiotic resistance genes within two different red swamp crayfish Procambarus clarkii cultivation ecosystems

Antibiotic resistance genes (ARGs) are emerging contaminants that pose a potential risk to human health worldwide. In this study, a metagenomic analysis was performed to investigate the distribution of ARGs in paddy field ecosystems, crayfish monoculture pond ecosystems, and rice-crayfish cultivation field ecosystems. The results showed that MacB and BcrA are two dominant ARGs, and macrolide is the dominant antibiotic not only in the water, but also in the sediment and gut of crayfish, in both the crayfish monoculture and the rice-crayfish cultivation ecosystems. Meanwhile, some lower-abundance ARGs in the water and sediment of crayfish cultivation ecosystems were significantly different in their abundance than those in rice paddy fields, and the ARGs in crayfish culture system and rice paddy fields showed even higher dissimilarities of diversity. Comprehensive analysis with redundancy analysis（RDA）and the distribution of dominant ARGs showed that the dissimilarity was related to the higher concentrations of total nitrogen (TN), total phosphorus (TP), chlorophyll a (Chla), permanganate index (COD_Mn), and nitrate in the water of rice paddy fields, and was related to the higher contents of N, P, K, and organic matter (OM) in the sediment of rice paddy fields. The source trackers of ARGs within the crayfish cultivation ponds and the rice-crayfish cultivation fields showed that the sediment in crayfish cultivation ponds mainly played the role of the 'sink' for ARGs, and the water and gut of crayfish mutually contributed to the high rates of ARGs. The ARG contribution rates of crayfish gut and sediment decreased and increased, respectively, in rice-crayfish cultivation fields and in crayfish monoculture ponds, which might be related to the lower crayfish biomass and the lower water depth in rice-crayfish cultivation fields.

Occurrence and distribution of antibiotics and corresponding antibiotic resistance genes in different soil types irrigated with treated wastewater

Diminishing freshwater (FW) supplies necessitate the reuse of treated wastewater (TWW) for various purposes, like irrigation of agricultural lands. However, there is a growing concern that irrigation with TWW may transfer antibiotic resistance genes (ARGs) to the soil and crops. We hypothesized that TWW irrigation would increase the prevalence of antibiotic residues together with the corresponding ARGs in the irrigated soil. We further predicted that soil texture, especially pH, clay content, and organic matter variabilities, would change the antibiotic residues concentrations and thus ARGs dissemination. To test our predictions, three soils types (loamy-sand, loam, and clay) were irrigated with two water types (FW and TWW), over two consecutive seasons. We monitored physico-chemical parameters, the abundance of seven antibiotic residues, and their corresponding ARGs together with class 1 integron (intI1) in 54 water and soil samples collected at the end of the field experiments. The results revealed increase in antibiotics concentrations and ARGs relative abundance in TWW than FW. Yet, in the soil ARGs relative abundances were independent of the irrigation water quality, but dependent on the soil type, especially the clay content. Further, there were no clear associations between the targeted antibiotics or the presence of heavy metals and ARGs' relative abundance in the water or soil samples. Therefore, our results question the link between the discharge of antibiotics and heavy metals, and the dissemination of ARGs in soil environments.

Hidden Resistome: Enrichment Reveals the Presence of Clinically Relevant Antibiotic Resistance Determinants in Treated Wastewater-Irrigated Soils

Treated-wastewater (TW) irrigation transfers antibiotic-resistant bacteria (ARB) to soil, but persistence of these bacteria is generally low due to resilience of the soil microbiome. Nonetheless, wastewater-derived bacteria and associated antibiotic resistance genes (ARGs) may persist below detection levels and potentially proliferate under copiotrophic conditions. To test this hypothesis, we exposed soils from microcosm, lysimeter, and field experiments to short-term enrichment in copiotroph-stimulating media. In microcosms, enrichment stimulated growth of multidrug-resistant Escherichia coli up to 2 weeks after falling below detection limits. Lysimeter and orchard soils irrigated in-tandem with either freshwater or TW were subjected to culture-based, qPCR and shotgun metagenomic analyses prior, and subsequent, to enrichment. Although native TW- and freshwater-irrigated soil microbiomes and resistomes were similar to each other, enrichment resulted in higher abundances of cephalosporin- and carbapenem-resistant Enterobacteriaceae and in substantial differences in the composition of microbial communities and ARGs. Enrichment stimulated ARG-harboring Bacillaceae in the freshwater-irrigated soils, whereas in TWW-irrigated soils, ARG-harboring γ-proteobacterial families Enterobacteriaceae and Moraxellaceae were more profuse. We demonstrate that TW-derived ARB and associated ARGs can persist at below detection levels in irrigated soils and believe that similar short-term enrichment strategies can be applied for environmental antimicrobial risk assessment in the future.

Antibiotic resistance development and human health risks during wastewater reuse and biosolids application in agriculture

The reuse of treated wastewater (TWW) and sewage sludge are considered as solutions to the limited water resource and sludge disposal issues, respectively. The associated environmental and human health risks need to be analyzed to assess whether they are safe solutions or not. This paper discusses issues that relate to the accumulation of antibiotics and antibiotic resistance (AR) determinants in agricultural lands and crops, following TWW irrigation and biosolid amendment. Exposure assessment and dose-response assessment are the two important aspects of risk assessment discussed in this paper. Finally, research gaps in current knowledge that are relevant to a comprehensive and quantitative AR risk assessment were identified which includes: 1.) Studies on soil conditions that increase the frequency of horizontal gene transfer (HGT) between native soil resistome and pathogenic microbes in biosolids and TWW 2.) Holistic studies that examine the accumulation or dissipation of antibiotics, antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from the irrigation/biosolids application stage to crop consumption stage 3.) The influences of soil environmental conditions (e.g. salinity, nutrients) on the fate of ARB and ARGs in soil and translocation in edible plants 4.) The development of dose-response models that explicitly incorporate the potential for ARGs transfer between microbes when quantifying the risks of infection due to ARB.

Critical insight into the fate of antibiotic resistance genes during biological treatment of typical biowastes

Antibiotic resistance genes (ARGs) in biowaste, such as livestock manure and excess activated sludge, pose potential threat to human and ecological health when applied to agricultural fields. Biological treatment approaches, such as thermophilic composting/vermicomposting and anaerobic digestion, widely adopted to stabilize biowaste have demonstrated significant effects on the fate of ARGs. However, the influence of these biological treatments on ARGs is not known. This review summarizes the occurrence of ARGs in biowaste and the impact of thermophilic composting, vermicomposting, and anaerobic digestion on the fate of ARGs with discussion on factors, including substrate properties, pretreatments, additives, and operational parameters, associated with ARGs during biological treatment of biowaste. Finally, this review explores the research implications and proposes new avenues in the field of biological treatment of organic waste.

Antibiotic resistance genes (ARGs) in agricultural soils from the Yangtze River Delta, China

As an important reservoir of intrinsic antimicrobial resistance, soil is subjected to increasing anthropogenic activities that creates sustained selection pressure for the prevalence of antibiotic resistance genes (ARGs), thus constituting an important environmental dissemination pathway to human exposure. This study investigated the levels and spatial distributions of three classes of ARGs in relation to a range of co-occurring chemical mixtures and soil properties at a regional scale of the Yangtze River Delta (YRD), China. The selected eight ARGs were all detected in 241 agricultural soil samples with relative abundances ranging from 1.01 × 10^-7 to 2.31 × 10^-1 normalized to the 16S rRNA gene. The sulII and tetG were the dominant ARGs with a mean relative abundance of 6.67 × 10^-3 and 5.25 × 10^-3, respectively. The ARGs were mainly present in agricultural soils alongside Taihu Lake and Shanghai municipality, the most agriculturally and economically vibrant area of the YRD region. Antibiotics, rather than other co-occurring pollutants and soil properties, remain to be the dominant correlate to the ARGs, suggesting their co-introduction into the soils via irrigation and manure application or the sustained selection pressure of antibiotics from these sources for the proliferation of ARGs in the soils. While the current dataset provided useful information to assess the ARGs pollution for mitigation, future studies are warranted to reveal the complete picture on the potential transfer of antimicrobial resistance from soil to agricultural produces to human consumption and associated health implications.

Combination of flow cytometry and molecular analysis to monitor the effect of UVC/H2O2 vs UVC/H2O2/Cu-IDS processes on pathogens and antibiotic resistant genes in secondary wastewater effluents

The efficiency of a new Advanced Oxidation Process (AOP), namely the photo Fenton like process UV-C/H₂O₂/IDS-Cu, in removing determinants of antibiotic resistance and pathogenic bacteria was compared to a consolidated AOP (namely UV-C/H₂O₂) in a secondary treated municipal WasteWater (WW). A reductionist experimental laboratory-based approach was applied on real WW and the parameters were collected by an alternative integrated approach using (i) flow cytometry to enumerate bacteria and test for the fitness of the bacterial communities and (ii) molecular analyses to define the community composition (16S rRNA amplicon sequencing) and the abundances of Antibiotic Resistance Genes (ARGs) and of the class 1 integron (intI1 gene) (by quantitative PCR). The same approach was applied also to post-treatment regrowth tests (24 h) to define the potential persistence of the tested parameters. These experiments were performed in both, human pathogens favorable conditions (HPC, in rich medium and 37°C) and in environmental mimicking conditions (EMC, original WW and 20°C). UV-C/H₂O₂/IDS-Cu process resulted to be more effective than the UV-C/H₂O₂in inactivating bacterial cells in the EMC post-treatment regrowth experiments. Both AOPs were efficiently abating potential human pathogenic bacteria and ARGs in the HPC regrowth experiments, although this trend could not be detected in the measurements taken immediately after the disinfection. In comparison with the UV-C/H₂O₂, the UV-C/H₂O₂/IDS-Cu process did not apparently offer significant improvements in the abatement of the tested parameters in the WW effluent but, by evaluating the results of the regrowth experiments it was possible to extrapolate more complex trends, suggesting contrasting efficiencies visible only after a few hours. This study offers a detailed view on the abatement efficiency of microbiological/genetic parameters for the UV-C/H₂O₂/IDS-Cu process, calling for technical adjustments for this very promising technology. At the same time, our results clearly demonstrated the inadequacy of currently applied methodologies in the evaluation of specific parameters (e.g. determinants of antibiotic resistance and pathogenic bacteria) in WW.