Risk Of Antibiotic Resistance Genes Research Articles

The environmental risk of antibiotic resistance genes from manure compost fertilizer gradually diminished during ryegrass planting

As one of the emerging pollutants in the environment, antibiotic resistance genes (ARGs) have attracted much attention. Composting is an effective way to reduce ARGs and the compost products were often used as soil amendments. However, the environmental risk of ARGs from compost products to soil and plants has not been well studied. Here, we assessed the environmental risk of ARGs from soil and ryegrass after applying manure composting. This study detected 21 different types of ARGs. Multidrug and tetracycline resistance genes were the most dominant ones, accounting for 39.2%/12.5% and 38.6%/11.6% in soil/ryegrass, respectively. This might be attributed to the decrease of Streptomyces, which is the potential host of multidrug and tetracycline ARGs. The environmental risk value, which was associated with mobile genetic elements (MGEs) and pathogens, increased in the soil and ryegrass, and return to the original level at the end of the growth cycle. The absolute environmental risk values of AH (high additive amount of the swine manure compost) and BH (high additive amount of the sheep manure compost) decreased by 0.0826 and 0.1505, respectively. The outcomes of this study revealed the environmental behavior and risk of ARGs transferring from compost to soil, and then entering into ryegrass, which is important to assess the environmental risk of compost and provide new insights into agricultural food safety.

Quantification of the mobility potential of antibiotic resistance genes through multiplexed ddPCR linkage analysis.

There is a clear need for global monitoring initiatives to evaluate the risks of antibiotic resistance genes (ARGs) towards human health. Therefore, not only ARG abundances within a given environment, but also their potential mobility, hence their ability to spread to human pathogenic bacteria needs to be quantified. We developed a novel, sequencing-independent method for assessing the linkage of an ARG to a mobile genetic element by statistical analysis of multiplexed droplet digital PCR (ddPCR) carried out on environmental DNA sheared into defined, short fragments. This allows quantifying the physical linkage between specific ARGs and mobile genetic elements, here demonstrated for the sulfonamide ARG sul1 and the Class 1 integron integrase gene intI1. The method's efficiency is demonstrated using mixtures of model DNA fragments with either linked and unlinked target genes: Linkage of the two target genes can be accurately quantified based on high correlation coefficients between observed and expected values (R2) as well as low mean absolute errors (MAE) for both target genes, sul1 (R2 = 0.9997, MAE = 0.71%, n = 24) and intI1 (R2 = 0.9991, MAE = 1.14%, n = 24). Furthermore, we demonstrate that adjusting the fragmentation length of DNA during shearing allows controlling rates of false positives and false negative detection of linkage. The presented method allows rapidly obtaining reliable results in a labor- and cost-efficient manner.

Effects of micron-scale zero valent iron on behaviors of antibiotic resistance genes and pathogens in thermophilic anaerobic digestion of waste activated sludge

This work investigated the metagenomics-based behavior and risk of antibiotic resistance genes (ARGs), and their potential hosts during thermophilic anaerobic digestion (TAD) of waste activated sludge, enhanced by micron-scale zero valent iron (mZVI). Tests were conducted with 0, 25, 100, and 250 mg mZVI/g total solids (TS). Results showed that up to 7.3% and 4.8% decrease in ARGs’ abundance and diversity, respectively, were achieved with 100 mg mZVI/g TS. At these conditions, ARGs with health risk in abundance and human pathogenic bacteria (HPB) diversity were also decreased by 8.3% and 3.6%, respectively. Additionally, mZVI reduced abundance of 72 potential pathogenic supercarriers for ARGs with high health risk by 2.5%, 5.0%, and 6.1%, as its dosage increased. Overall, mZVI, especially at 100 mg/g TS, can mitigate antibiotic resistance risk in TAD. These findings are important for better understanding risks of ARGs and their pathogenic hosts in ZVI-enhanced TAD of solid wastes.

Iron-modified peat and magnetite-pine bark biosorbents for levofloxacin and trimethoprim removal from synthetic water and various pharmaceuticals from real wastewater

Humans are at significant risk of antibiotic resistance genes (ARGs) and antimicrobial resistance (AMR) via exposure to pharmaceutical contaminants in water, so there is a strong need for cost-effective environmental solutions to mitigate this crisis. This study introduces iron-modified peat and magnetite-pine bark as efficient, low-cost and green biosorbents for the adsorption of pharmaceutical contaminants from wastewater. Peat biomass, modified by iron extracted from a groundwater treatment sludge was dissolved in acid to prepare the iron-modified peat biosorbent, and pine (Pinus sylvestris) bark as a forest industry by-product was mixed with iron salts (Fe3+: Fe2+ = 2:1) to obtain the magnetite biosorbent. The adsorption of levofloxacin was little influenced by pH compared to trimethoprim. The equilibrium removal efficiency of antibiotics over both biosorbents was reached after 180 min contact time. The maximum adsorption capacity over iron-modified peat was about 200 mg/g for both antibiotics and over magnetite-pine bark 153.0 mg/g for levofloxacin and 184.1 mg/L for trimethoprim. Possible antibiotic adsorption mechanisms were proposed based on the Fourier transform infrared spectroscopy (FTIR) analysis. Experiments with real wastewater effluent revealed trimethoprim removal of 56.6–84.3% (dosage: 3 g/L). Moreover, a variety of other pharmaceuticals were removed by the biosorbents.

Composting reduces the risks of antibiotic resistance genes in maize seeds posed by gentamicin fermentation waste

Using high-throughput quantitative PCR and next generation sequencing, the impact of land application of raw and composted gentamicin fermentation waste (GFW) on antibiotic resistance genes (ARGs) in maize seeds was studied in a three-year field trial. The raw and composted GFW changed both the bacterial community composition and the ARGs diversity in the maize seeds compared to non-amended controls and chemical fertilizer. The abundance of ARGs after raw GFW amendment was significantly higher than other treatments because of a high abundance of aadA1, qacEdeltal and aph(2′)-Id-02; probably induced by gentamicin selection pressure in maize tissues. Meanwhile, the potential host of these three ARGs, pathogenic bacteria Tenacibaculum, also increased significantly in maize seeds after the application of raw GFW. But our result proved that composting could weaken the risk posed by GFW. We further reveal that the key biotic driver for shaping the ARG profiles in maize seeds is bacterial community followed by heavy metal resistance genes, and ARGs are more likely located on bacterial chromosomes. Our findings provide new insight into ARGs dispersal mechanism in maize seeds after long-term GFW application, demonstrate the potential benefits of composting the GFW to reduce risks as well as the potential efficient management method to GFW.

Leaching risk of antibiotic resistance contamination from organic waste compost in rural areas

Composting is an important decentralized technology for treating multiple biodegradable organic wastes in rural areas. However, compared to industrial composting (i.e., time and temperature protocols), rural composting is less well-controlled, and the risk of antibiotic resistance genes (ARGs) in these composts needs to be determined. We performed a quantitative determination of ARGs and both prokaryotes and eukaryotes to investigate the liquid-solid leaching ratio and the relationship between ARGs and microbial communities in solid and water extracts of composts collected from rural areas. We observed a high level of sulfonamides resistance genes and tetracyclines resistance genes (10−4−10−2 copies/16S copies). Tet-C and tet-X show the strongest leaching potential in rural organic waste composts with complex hosts in solid and liquid phases. This study showed high ARG abundances in compost solid and water extracts, highlighting the leaching risk of compost ARGs when exposed to runoff or groundwater during open storage and field application.

Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes

Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), β-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.

Sustainable conversion of antibiotic wastewater using microbial fuel cells: Energy harvesting and resistance mechanism analysis

In this study, tetracycline (TC) can be degraded in microbial fuel cells (MFCs) rapidly and efficiently for the synergistic effect of microbial metabolism and electrical stimulation. Different TC concentrations had different effects on the bioelectric performance of MFCs. Among them, 10 mg/L TC promoted the bioelectric properties of MFCs, the maximum power density reached 1744.4 ± 74.9 mW/cm2. In addition, we demonstrated that Geobacter and Chryseobacterium were the dominant species in the anode biofilm, while Azoarcus and Pseudomonas were the prominent species in the effluent, and the initial TC concentration affected the microbial community composition. Furthermore, the addition of TC increased the relative abundance of aadA3, sul1, adeF, cmlA, and tetC in reactors, indicating that a single antibiotic could promote the expression of self-related resistance as well as the expression of other ARGs. Moreover, the presence of TC can increase the relative content of mobile genetic elements (MGEs) and greatly increase the risk of antibiotic resistance genes (ARGs) spreading. Meanwhile, network analysis revealed that some microorganisms (such as Acidovorax caeni, Geobacter soil, and Pseudomonas thermotolerans) and MGEs may be potential hosts for multiple ARGs.

Enzymatic pretreatment mitigates the dissemination of antibiotic resistance genes via regulating microbial populations and gene expressions during food waste fermentation

Food waste (FW) has been recognized as essential reservoir for resource recovery via anaerobic fermentation, which could also bring the potential risk of antibiotic resistance genes (ARGs) dissemination. Although the structural deficiency of FW could be stimulated by enzymatic pretreatment to enhance fermentation efficiency, the influences of enzymatic pretreatment on ARGs fate and microbial metabolic pathways involved in ARGs dissemination have rarely been reported. This work proved that enzymatic pretreatment could effectively decrease the total abundance of ARGs (reduced by 13.8%-24.5%) during long-term FW fermentation. It was found that enzymatic pretreatment significantly reduced the ARGs belonging to the efflux pump, which might be ascribed to its ability to increase membrane permeability. Furthermore, enzymatic pretreatment was in favor of reducing microbial diversity and various potential ARGs host (e.g., Methanosarcina, Clostridium, Prevotella, Parabacteroides). Also, this pretreatment remarkably up-regulated the genetic expressions involved in ABC transporter (e.g., eryF and mntA) and down-regulated the genetic expressions that participated in DNA replication, two-component systems (e.g., uphA and cckA), and quorum sensing (e.g., rpfF and lsrG), thereby decreasing ARGs transmission. This study would expand the insight of the influences of pretreatment method on ARGs fate during FW fermentation, and offer practical guidance on the sustainable management of FW.

Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6′)-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6′)-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.

Metagenomic analysis revealed sources, transmission, and health risk of antibiotic resistance genes in confluence of Fenhe, Weihe, and Yellow Rivers

Rivers are important vectors and reservoirs of antibiotics resistance genes (ARGs). Information regarding transmission and health risk of ARGs in river confluence is still lacking. In this study, metagenomics was used to distinguish contributions of human activities on ARGs and human pathogenic bacteria (HPB) in confluence of Fenhe, Weihe, and Yellow Rivers. Bacitracin resistance gene and bacA were the highest in all rivers, with 1.86 × 10−2-7.26 × 10−2 and 1.79 × 10−2-9.12 × 10−2 copies/16S rRNA copies, respectively. River confluence significantly increased the abundance of ARGs, especially at the confluence of three rivers with the highest 1.53 × 10−1 copies/16S rRNA copies. Antibiotic efflux and antibiotic target alteration were the dominant resistant mechanisms in three rivers. ARGs profiles were influenced by multiple factors, with the contributions of various factors ranked as microbial communities > physicochemical factors > human activities > mobile genetic elements (MGEs). Notably, human activities and animal feces were important potential contributors of ARGs in the Weihe River and Yellow River. Transposons, as the main MGEs in three rivers, played important roles in ARGs transfer. The confluence of three rivers had the highest abundance of MGEs with the greatest transfer potentials, and therefore exhibiting the largest exposure risk of ARGs with 232.4 copies/cap·d. Furthermore, correlations of ARGs, MGEs, and HPB in different rivers were constructed via co-occurrence modes to systematically illustrate the health risks of ARGs. This study firstly unveiled the transmission and health risk of ARGs in river confluence, providing supports for ARGs control in watershed.

Sensitive response mechanism of ARGs and MGEs to initial designed temperature during swine manure and food waste co-composting

The rapid aerobic composting process has been used to reduce organic wastes, but the associated risks of antibiotic resistance genes (ARGs) need to evaluate in an efficient way. The primary objective of this work was to explore the underlying mechanism of initial adjustment in composting temperature on the variation of ARGs, mobile genetic elements (MGEs), and microbial composition during co-composting. The co-composting was initially externally heated (T2) for 5 days. The results showed that ARGs abundance in conventional composting (T1) was reduced by 49.36%, while multidrug was enriched by 86.16% after a period of 30 days. While in T2 ARGs were removed by 79.46% particularly the fraction of sulfonamide, multidrug, and vancomycin resistance genes were >90% without rebounding of any ARGs. Whereas, MGEs were reduced by 68.12% and 93.62% in T1 and T2, while the half-lives of ARGs and MGEs were lower in T2 compared to T1 (86.3%,86.7%). T2 also affected the metabolism function by regulating carbohydrate metabolism (9.62–10.39%) and amino acid metabolism (9.92–10.93%). Apart from this, the potential human pathogenic bacteria Pseudomonas was reduced by 90.6% in T2 and only 32.9% in T1 respectively. Network analysis showed that Ureibacillus, Weissella, Corynebacterium, Escherichia-Shigella, Acinetobacter were the main host of multiple genes. Structural equation models exhibited that bacterial communities were mainly responsible for the enrichment of ARGs in T1, whereas, it was directly affected by MGEs in T2. Similarly, ARGs variation was directly related to composting temperature. With this simple strategy, ARGs associated risk can be significantly reduced in composting.

Climate and nutrients regulate biographical patterns and health risks of antibiotic resistance genes in mangrove environment

Mangroves are prone to receive pollutants and act as a sink for antibiotic resistance genes (ARGs). However, knowledge of the human health risk of ARGs and its influencing factors in mangrove ecosystems is limited, particularly at large scales. Here, we applied a high-throughput sequencing technique combined with an ARG risk assessment framework to investigate the profiles of ARGs and their public health risks from mangrove wetlands across South China. We detected 456 ARG subtypes, and found 71 of them were identified as high-risk ARGs, accounting for 0.25 % of the total ARG abundance. Both ARGs and bacterial communities showed a distance-decay biogeography, but ARGs had a steeper slope. Linear regression analysis between features of co-occurrence network and high-risk ARG abundance implies that greater connections in the network would result in higher health risk. Structural equation models showed that geographic distance and MGEs were the most influential factors that affected ARG patterns, ARGs and MGEs contributed the most to the health risk profiles in mangrove ecosystems. This work provides a novel understanding of biogeographic patterns and health risk assessment of ARGs in mangrove ecosystems and can have profound significance for mangrove environment management with regard to ARG risk control.

Metagenomic assembly reveals the circadian oscillations of the microbiome and antibiotic resistance genes in a model of laying hens.

The increasing risks of antibiotic resistance genes (ARGs) in livestock feces have attracted global attention. However, how the rhythmic activity of ARGs changes in fecal microbiota remains largely unclear. In our study, we collected 52 fresh fecal samples every 6 h over 72 h from laying hens and characterized circadian oscillations of bacteria and ARGs using an approach based on assembled metagenome shotgun sequencing. We found that 14% of commensal bacterial taxonomic units fluctuated over 24 h. A total of 33 out of 281 ARGs and 17 of 574 mobile genetic elements (MGEs) featured rhythmic patterns in feces. lnuC and ANT(6)H-lb were the two most abundant ARGs with circadian oscillation identified from feces, and they increased during the day and decreased at night. Acetate, butyrate, propionate, and 78 out of 392 MetaCyc pathways relating to short-chain fatty acid (SCFA) metabolism featured circadian oscillations. Assessment of the above ARG-other element connections revealed that 17 ARGs presented strong correlations with 7 MGEs, and 2 SCFAs (acetate and propanoate) and bacterial species in feces. Structural equation model (SEM) analysis showed that ARGs were directly affected by microbial β-diversity and MGEs. These results showed a comprehensive map of ARGs over 24 h and revealed circadian oscillations of ARGs, which are influenced by key bacterial species, MGEs, and metabolites. Together, our findings advance comprehension of circadian oscillations of ARGs in the fecal microbiota and provide a reference for ARGs control and management.

Leaching risks of antibiotic resistance genes in urban underlying surface sediments during the simulated stormwater runoff and its controls

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, no available literature could be found on ARGs leaching from urban underlying surface sediments during stormwater runoff. In this study, surface sediments from commercial public squares around Nanjing (China) was selected for the investigation of target ARGs leaching kinetics, showing that absolute abundances of target ARGs desorption reached at the equilibrium during leaching time of 120-240min with all of the desorption efficiencies about 30%, indicating that there would be low proportion of leaching ARGs in the total ARGs migrating with runoff during rainfall events. Five target ARGs leaching including intI1 (clinic), strA, strB, tetM and tetX can be better described by the pseudo-second-order equation, while qacEdelta1 leaching can be better described by the pseudo-first-order equation, and the leaching for both sul1 and sul2 can be well described by the pseudo-first-order and pseudo-second-order equations. The effects of environmental factors including S/L ratios, pH values and water temperatures indicated that leaching efficiencies of target ARGs enhanced significantly with the increase of S/L ratios and water temperatures, but decreased with the increase of pH values. The transmission experiments after the simulated solar irradiation and heat implied that both large solar UV irradiation (30W/m2) and high temperature (40℃) were conducive to conjugation and transformation frequencies of ARGs. Furthermore, both high Cao and medium PAM levels could be effective for blocking ARGs transmission in the leachate from underlying surface sediments.

Research advances in ecological risk of antibiotic resistance genes

Antibiotics have played an important role in the prevention and treatment of human and animal diseases as well as the improvement of animal products. However, the mass products and application of antibiotics, especially the abuse in animal industry and clinical medicine, led to the widespread of antibiotic resistance genes (ARGs) in the environment. They spread widely through conjugation, transposition, and transformation with the help of movable elements such as plasmid, transposon and integrons, resulting in the continuous enhancement of microbial medicinal properties and posing a serious threat to human health and ecological security. At present, great attention has been paid to the impacts of ARGs on human health, but limited research on the ecological risk of ARGs in the environment. Here, the status quo and ecological risks of ARGs pollution were summarized, and the future research priorities in this field were prospected. We hope it could pave the way for further studies and give references for the ecological control and prevention of ARGs pollution.

Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils

The application of livestock manure increases the dissemination risk of antibiotic resistance genes (ARGs) in farmland soil environment. However, the vertical migration behavior and driving factor of ARGs in manured soil under swine manure application remains undefined. Here, the dynamics of ARGs, mobile genetic elements (MGEs) and bacterial communities in different soil depths (0 – 80 cm) with long-term swine manure application were tracked and conducted using real-time qPCR. Results showed that long-term application of swine manure remarkably facilitated the vertical accumulation of ARGs and MGEs, in particular that the relative abundance of blaampC showed significant enrichment with increasing depth. ARGs abundance was similar in the three fields with long-term application of swine manure. (p＞0.05). Procrustes analysis indicated that microbial communities were the dominant drivers of ARGs variation in topsoil, and the changes of environmental factors played a vital role in vertical migration ARGs in cropland soils. Additionally, the variation patterns of high-risk ARGs (i.e., blaampC, blaTEM-1) were influenced by the dominant bacteria (Actinomycetes) and pH. This study illustrated that the swine manure application promoted the vertical migration of ARGs, including multidrug resistance determinants, highlighting the ecological risk caused by long-term manure application.

Assessment of global health risk of antibiotic resistance genes

Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health.

Composting Reduces the Risks of Antibiotic Resistance Genes in Maize Seeds Posed by Gentamicin Fermentation Waste

Composting Reduces the Risks of Antibiotic Resistance Genes in Maize Seeds Posed by Gentamicin Fermentation Waste

The Environment Risk of Antibiotic Resistance Genes from Manure Compost Fertilizer Gradually Diminished During Ryegrass Planting

The Environment Risk of Antibiotic Resistance Genes from Manure Compost Fertilizer Gradually Diminished During Ryegrass Planting